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Honda civic 2006 battery dead (immobilizer issue)

Old Mar 30, 2018
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Honda civic 2006 battery dead (immobilizer issue)

Hi, i had left my honda civic 2006 in a place for a month now . After i tried to switch the engine on the battery was completely dead. After jump starting my car, the car switches off again and green color key light flashes on the dash. I surfed through google and it shows that the problem is with the immobilzer and the codes or the programming has been erased. Can any one help?
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Old Mar 30, 2018
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Re: Honda civic 2006 battery dead (immobilizer issue)

Try this because it may be out of synch with the locks/key/battery

-lock the car, just as it was when you found it.
-disconnect the battery for 20 minutes so the ecu resets.
-reconnect the (hopefully charged) battery
-unlock the doors with the fob
-start the car.
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Old Mar 30, 2018
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Re: Honda civic 2006 battery dead (immobilizer issue)

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Old Mar 30, 2018
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Re: Honda civic 2006 battery dead (immobilizer issue)

Some of those cars had to have the drivers fusebox replaced and programmed to correct that problem....
I think the bulletin about it has been posted or linked in this forum before
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Old Jul 5, 2021
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Smile Re: Honda civic 2006 battery dead (immobilizer issue)

You are lucky if you find this post. I had exactly the same problem! The actual fix itself took literally only 5 seconds. All the advice I found on the web did not work. Things like pressing the panic button for 5 seconds and unlock with remote, or unlocking the car with the physical key did nothing. In hindsight, this was because of the ecu having corrupt data after the battery went dead and got jumped started afterwards. It's outrageous that the Honda ecu is so fragile that such a standard event would result in ecu data corruption. Guess that's a good way for dealership to make huge profits. Also, all the "key programmers" by themselves (ck100 or sbb) are not enough to fix the problem. They can program in new keys and the remote might be made to work, but the code that instructs the ecu to release the immobilizer lock was corrupt. And you still can't start the car even if you can unlock the car doors with the remote. So the simple cheap fix is to get a under $100 obd plug like the Thinkdiag. Insert it into the obd port, and choose "Immobilizer Status". If it says "Status Abnormal", it gives you the option to reset the Ecu or reset something like "mipiu / se" (sorry, I forgot the exact acronym the machine displayed). The exact name does not matter. It simply will guide you and tell you exactly what to do step by step. If it says "Immobilizer Normal", then you can proceed to choose "all keys lost", and it will guide you through re-adding your existing keys to the computer. You can also use high end obd scanners like Autel Maxisys, or X431 to do the same, but they cost around $1k. The trick is to make sure that your obd tool can do "Ecu / Mipiu / Muipse" (or whatever name they use to mean the same) reset, or something similar. I don't think the Android Torque Pro can do that. If you know an Android or IOS app that can code Ecu and program in new keys, then do post it here to help save the world! The typical obd tools cannot do that, because they can only Read data, and cannot do "Ecu coding". As said, the only Ecu coding capable App or tool I found is the Thinkdiag, which was around $80 , which includes 1st year subscription. It's sold everywhere and can be found with a simple google search. But if you can find something else that does the same, it should work too. Again, if you don't reset the Ecu, then no amount of key programming would fix the problem. If your locksmith does not know that, don't here him! You'll be wasting your money. If none of that works, then just change the Ecu ($25 on ebay) (as easy as changing a car tire, and there are plenty of youtube tutorials on that). After you put in a new Ecu, you still need a Thinkdiag or Autel or X431 to: a) update the Vin, and b) add in your keys by choosing "Immobilizer". In most cases, you don't need to replace the Ecu. I am sharing all that because I was in so much despair after days of surfing for a fix to no avail, and I was about to send my car to the junk yard. Some lucky guy would have bought it for $1 and fixed it in 5 seconds. The misleading info you find on the web made me to think that there was no fix unless you spend $1000 to toll the car to the dealer to get them to unlock the car. The car itself is old and is not worth that much to justify spending that. A locksmith will do the same for you, and probably charge $200 for it. So spending approx. $80 on a Thinkdiag is cheaper, and you can use the same tool to be a good Samaritan, and help other people fix similar problems, or to become a car locksmith yourself. I think that the same method works for all cars, just not this model. But some cars also have "PIN", which the machines I mentioned can also decode, depending on the year. If you call up several car locksmiths and they all say they can unlock your year and model of car, it probably means that they will come and use their Thinkdiag/Autel/X431 and do the same for you. If they ALL say for sure that your year and model has pins that cannot be decoded no matter how much you pay them, then it's possible that other solutions are needed. Some recent models of cars have pins that those machines cannot "yet" fix until updates are available. But for older cars, a working ecu coder with built in key programming will fix the car in 5 seconds.
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Old Aug 21, 2022
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Re: Honda civic 2006 battery dead (immobilizer issue)

Originally Posted by aacarwiz
You are lucky if you find this post. I had exactly the same problem! The actual fix itself took literally only 5 seconds. All the advice I found on the web did not work. Things like pressing the panic button for 5 seconds and unlock with remote, or unlocking the car with the physical key did nothing. In hindsight, this was because of the ecu having corrupt data after the battery went dead and got jumped started afterwards. It's outrageous that the Honda ecu is so fragile that such a standard event would result in ecu data corruption. Guess that's a good way for dealership to make huge profits. Also, all the "key programmers" by themselves (ck100 or sbb) are not enough to fix the problem. They can program in new keys and the remote might be made to work, but the code that instructs the ecu to release the immobilizer lock was corrupt. And you still can't start the car even if you can unlock the car doors with the remote. So the simple cheap fix is to get a under $100 obd plug like the Thinkdiag. Insert it into the obd port, and choose "Immobilizer Status". If it says "Status Abnormal", it gives you the option to reset the Ecu or reset something like "mipiu / se" (sorry, I forgot the exact acronym the machine displayed). The exact name does not matter. It simply will guide you and tell you exactly what to do step by step. If it says "Immobilizer Normal", then you can proceed to choose "all keys lost", and it will guide you through re-adding your existing keys to the computer. You can also use high end obd scanners like Autel Maxisys, or X431 to do the same, but they cost around $1k. The trick is to make sure that your obd tool can do "Ecu / Mipiu / Muipse" (or whatever name they use to mean the same) reset, or something similar. I don't think the Android Torque Pro can do that. If you know an Android or IOS app that can code Ecu and program in new keys, then do post it here to help save the world! The typical obd tools cannot do that, because they can only Read data, and cannot do "Ecu coding". As said, the only Ecu coding capable App or tool I found is the Thinkdiag, which was around $80 , which includes 1st year subscription. It's sold everywhere and can be found with a simple google search. But if you can find something else that does the same, it should work too. Again, if you don't reset the Ecu, then no amount of key programming would fix the problem. If your locksmith does not know that, don't here him! You'll be wasting your money. If none of that works, then just change the Ecu ($25 on ebay) (as easy as changing a car tire, and there are plenty of youtube tutorials on that). After you put in a new Ecu, you still need a Thinkdiag or Autel or X431 to: a) update the Vin, and b) add in your keys by choosing "Immobilizer". In most cases, you don't need to replace the Ecu. I am sharing all that because I was in so much despair after days of surfing for a fix to no avail, and I was about to send my car to the junk yard. Some lucky guy would have bought it for $1 and fixed it in 5 seconds. The misleading info you find on the web made me to think that there was no fix unless you spend $1000 to toll the car to the dealer to get them to unlock the car. The car itself is old and is not worth that much to justify spending that. A locksmith will do the same for you, and probably charge $200 for it. So spending approx. $80 on a Thinkdiag is cheaper, and you can use the same tool to be a good Samaritan, and help other people fix similar problems, or to become a car locksmith yourself. I think that the same method works for all cars, just not this model. But some cars also have "PIN", which the machines I mentioned can also decode, depending on the year. If you call up several car locksmiths and they all say they can unlock your year and model of car, it probably means that they will come and use their Thinkdiag/Autel/X431 and do the same for you. If they ALL say for sure that your year and model has pins that cannot be decoded no matter how much you pay them, then it's possible that other solutions are needed. Some recent models of cars have pins that those machines cannot "yet" fix until updates are available. But for older cars, a working ecu coder with built in key programming will fix the car in 5 seconds.
I verified Thinkdiag fixed the excat same issue on my civic 06. Here is the ebay link I bought the diagnostic tool https://www.ebay.com/itm/38369572139...Cclp%3A2563228
Plug Thinkdiag on the obd2 port in your car, once connected, open the app from your smartphone, choose maintenance functions-->IMMO-->REPLACE MPCS/MICU/IMOES, follow the instructions to turn off ignition then turn on ignition, then the immobilizer will be reset and keys worked again.
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Old Apr 1, 2023
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Re: Honda civic 2006 battery dead (immobilizer issue)

Originally Posted by aacarwiz
You are lucky if you find this post. I had exactly the same problem! The actual fix itself took literally only 5 seconds. All the advice I found on the web did not work. Things like pressing the panic button for 5 seconds and unlock with remote, or unlocking the car with the physical key did nothing. In hindsight, this was because of the ecu having corrupt data after the battery went dead and got jumped started afterwards. It's outrageous that the Honda ecu is so fragile that such a standard event would result in ecu data corruption. Guess that's a good way for dealership to make huge profits. Also, all the "key programmers" by themselves (ck100 or sbb) are not enough to fix the problem. They can program in new keys and the remote might be made to work, but the code that instructs the ecu to release the immobilizer lock was corrupt. And you still can't start the car even if you can unlock the car doors with the remote. So the simple cheap fix is to get a under $100 obd plug like the Thinkdiag. Insert it into the obd port, and choose "Immobilizer Status". If it says "Status Abnormal", it gives you the option to reset the Ecu or reset something like "mipiu / se" (sorry, I forgot the exact acronym the machine displayed). The exact name does not matter. It simply will guide you and tell you exactly what to do step by step. If it says "Immobilizer Normal", then you can proceed to choose "all keys lost", and it will guide you through re-adding your existing keys to the computer. You can also use high end obd scanners like Autel Maxisys, or X431 to do the same, but they cost around $1k. The trick is to make sure that your obd tool can do "Ecu / Mipiu / Muipse" (or whatever name they use to mean the same) reset, or something similar. I don't think the Android Torque Pro can do that. If you know an Android or IOS app that can code Ecu and program in new keys, then do post it here to help save the world! The typical obd tools cannot do that, because they can only Read data, and cannot do "Ecu coding". As said, the only Ecu coding capable App or tool I found is the Thinkdiag, which was around $80 , which includes 1st year subscription. It's sold everywhere and can be found with a simple google search. But if you can find something else that does the same, it should work too. Again, if you don't reset the Ecu, then no amount of key programming would fix the problem. If your locksmith does not know that, don't here him! You'll be wasting your money. If none of that works, then just change the Ecu ($25 on ebay) (as easy as changing a car tire, and there are plenty of youtube tutorials on that). After you put in a new Ecu, you still need a Thinkdiag or Autel or X431 to: a) update the Vin, and b) add in your keys by choosing "Immobilizer". In most cases, you don't need to replace the Ecu. I am sharing all that because I was in so much despair after days of surfing for a fix to no avail, and I was about to send my car to the junk yard. Some lucky guy would have bought it for $1 and fixed it in 5 seconds. The misleading info you find on the web made me to think that there was no fix unless you spend $1000 to toll the car to the dealer to get them to unlock the car. The car itself is old and is not worth that much to justify spending that. A locksmith will do the same for you, and probably charge $200 for it. So spending approx. $80 on a Thinkdiag is cheaper, and you can use the same tool to be a good Samaritan, and help other people fix similar problems, or to become a car locksmith yourself. I think that the same method works for all cars, just not this model. But some cars also have "PIN", which the machines I mentioned can also decode, depending on the year. If you call up several car locksmiths and they all say they can unlock your year and model of car, it probably means that they will come and use their Thinkdiag/Autel/X431 and do the same for you. If they ALL say for sure that your year and model has pins that cannot be decoded no matter how much you pay them, then it's possible that other solutions are needed. Some recent models of cars have pins that those machines cannot "yet" fix until updates are available. But for older cars, a working ecu coder with built in key programming will fix the car in 5 seconds.
wow. thank you. you are the saviour.

i had same problem. my 06 civic hybrid had same problem. car was sitting idle for 5 months. battery died. i jump started it then it started. after 30 mins drive, i parked it. but then it did not start next day. even jump starting it not helpful. green key symbol blinks but no cranking. so i changed battery thinking it will solve. but again green key symbol blinks no cranking. so i searched on net everywhere. found that it is immobilizer issue but do not know how to resolve it. finally i saw your post. ordered thinkdiag obd2 scanner like you said. registered account. activated it. followed instructions on the manual to install app and update. then connected it to obd2 port. then went to maintenance functions-->IMMO-->REPLACE MPCS/MICU. followed instructions to turn on ignition and turn off then green key gone. i am able to start it immediately. both keys starts car now.

i never used obd2 scanner before. first time used because of you and my experience with car is limited to changing punctured tire. but i tried and got success. very satisfying. Thank you for your help.
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Old Aug 8, 2023
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Re: Honda civic 2006 battery dead (immobilizer issue)

Originally Posted by aacarwiz
You are lucky if you find this post. I had exactly the same problem! The actual fix itself took literally only 5 seconds. All the advice I found on the web did not work. Things like pressing the panic button for 5 seconds and unlock with remote, or unlocking the car with the physical key did nothing. In hindsight, this was because of the ecu having corrupt data after the battery went dead and got jumped started afterwards. It's outrageous that the Honda ecu is so fragile that such a standard event would result in ecu data corruption. Guess that's a good way for dealership to make huge profits. Also, all the "key programmers" by themselves (ck100 or sbb) are not enough to fix the problem. They can program in new keys and the remote might be made to work, but the code that instructs the ecu to release the immobilizer lock was corrupt. And you still can't start the car even if you can unlock the car doors with the remote. So the simple cheap fix is to get a under $100 obd plug like the Thinkdiag. Insert it into the obd port, and choose "Immobilizer Status". If it says "Status Abnormal", it gives you the option to reset the Ecu or reset something like "mipiu / se" (sorry, I forgot the exact acronym the machine displayed). The exact name does not matter. It simply will guide you and tell you exactly what to do step by step. If it says "Immobilizer Normal", then you can proceed to choose "all keys lost", and it will guide you through re-adding your existing keys to the computer. You can also use high end obd scanners like Autel Maxisys, or X431 to do the same, but they cost around $1k. The trick is to make sure that your obd tool can do "Ecu / Mipiu / Muipse" (or whatever name they use to mean the same) reset, or something similar. I don't think the Android Torque Pro can do that. If you know an Android or IOS app that can code Ecu and program in new keys, then do post it here to help save the world! The typical obd tools cannot do that, because they can only Read data, and cannot do "Ecu coding". As said, the only Ecu coding capable App or tool I found is the Thinkdiag, which was around $80 , which includes 1st year subscription. It's sold everywhere and can be found with a simple google search. But if you can find something else that does the same, it should work too. Again, if you don't reset the Ecu, then no amount of key programming would fix the problem. If your locksmith does not know that, don't here him! You'll be wasting your money. If none of that works, then just change the Ecu ($25 on ebay) (as easy as changing a car tire, and there are plenty of youtube tutorials on that). After you put in a new Ecu, you still need a Thinkdiag or Autel or X431 to: a) update the Vin, and b) add in your keys by choosing "Immobilizer". In most cases, you don't need to replace the Ecu. I am sharing all that because I was in so much despair after days of surfing for a fix to no avail, and I was about to send my car to the junk yard. Some lucky guy would have bought it for $1 and fixed it in 5 seconds. The misleading info you find on the web made me to think that there was no fix unless you spend $1000 to toll the car to the dealer to get them to unlock the car. The car itself is old and is not worth that much to justify spending that. A locksmith will do the same for you, and probably charge $200 for it. So spending approx. $80 on a Thinkdiag is cheaper, and you can use the same tool to be a good Samaritan, and help other people fix similar problems, or to become a car locksmith yourself. I think that the same method works for all cars, just not this model. But some cars also have "PIN", which the machines I mentioned can also decode, depending on the year. If you call up several car locksmiths and they all say they can unlock your year and model of car, it probably means that they will come and use their Thinkdiag/Autel/X431 and do the same for you. If they ALL say for sure that your year and model has pins that cannot be decoded no matter how much you pay them, then it's possible that other solutions are needed. Some recent models of cars have pins that those machines cannot "yet" fix until updates are available. But for older cars, a working ecu coder with built in key programming will fix the car in 5 seconds.
OMG I am sooooo thankful for this thread! This 100% worked for me. I was able to accomplish this with this tool:
Amazon Amazon
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