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Before I went to a mechanic to certify the car, it was working just fine, this problem had not occurred at all. The car could be driven just fine with no problems. However, once I had to go to a mechanic to certify the car, they said that a few things had to be fixed. I thought that was acceptable, but once they fixed it, and I came to pick it up, it wasn't able to start precisely because of this flashing green key light on the dashboard that showed up.

The mechanic was able to get it working once by placing the key in the ignition and turning on and off the ignition a few times, but once I came home with the car, it stopped working the day after, and the flashing green key light on the dashboard still shows up. I had a locksmith come and look at the car and they said it was a problem with the car for some reason.

I have exactly the same problem when I use my spare key.

What can I do to fix this issue?

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There are a few possibilities that cause intermittent issues with the immobilizer. Here are a few I run into with 1 being the most common.

  1. The key gets damaged. If its the remote head key then this year/model uses an integrated circuit for keyless entry and transponder. Its very common that the antenna for the transponder gets broken/loose solder joints. Its also common they suffer water damage and the circuit fails completely. Both of these can causes intermittent failures of the code being transmitted.

  2. Low car battery. The immobilizer system on Honda's do not like to work with low voltage. ( If the locksmith tried making a new key then I would probably lean to this one being your problem or #3.)

  3. The immobilizer/key antenna around the ignition starts to fail.

  4. Water damage in MUX. (interior fuse box)

  5. Wiring/grounding issue's in any one of the modules that are part of the immobilizer chain. (IMMO,MUX,ECU)

Something you can try is to bridge pins 4 & 5 of the OBD2 port with a paper clip. There is a known grounding issue with some of these cars that this is a temporary fix for. I don't know the full gyst of it but if bridging the pins work then its easy to google the full fix for it. I have had to bridge a few for my repo clients. Maybe the mechanic removed the a previous bridge to hook in their scan tool. It causes similar issue's with the immobilizer along with a slew of other oddities.

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Sounds like a dead button cell battery in your key to me. Do you have a second key you can try?

EDIT: In my Mazda I get the flashing green key symbol with a dead key fob battery when trying to use the keyless starting feature and have to start the car with the actual key. I thought the OP may have had the same kind of system. According to @narkeleptk Honda's use the green key to represent a problem with the immobilizer, so my answer is not relevant to this question

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  • The battery in keyless entry remote does not effect the immobilizer. The transponder that is built into the fob is still powered by the antenna coil.
    – narkeleptk
    Nov 23, 2020 at 22:36
  • That's correct I believe. Admittedly I am not familiar with the 2006 Civic, But I know in my case with a Mazda CX-9, I can't use the keyless start feature with a dead battery in the fob. I also just get a flashing green key on the dash. I can however remove the ignition switch cover and use the actual key to start the vehicle. The way the OP worded the question saying the mechanic "placed the key inside" made me think the issue could be trying to use keyless start with a dead fob battery. I will update my answer.
    – David Watson
    Nov 23, 2020 at 22:56
  • The mazda's green light is totaly different then the honda's green light. In your mazda its a message related to the proximity keys signal which would have to do with the battery. The immobilizer uses a red light for you. For honda's the green light is only for immobilizer. No keyless start for honda's on these years.
    – narkeleptk
    Nov 23, 2020 at 22:59
  • Fair enough. I stand corrected. Thanks for clearing that up.
    – David Watson
    Nov 23, 2020 at 23:02

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