Honda Civic owners have reported 2 problems related to anti-theft controller (under the electrical system category). The most recently reported issues are listed below. Also please check out the statistics and reliability analysis of Honda Civic based on all problems reported for the Civic.
Should you happen to lose battery power, Honda's "immobilizer" anti-theft system will lose its memory and unable to recognize the owner's keys. Honda's solution is to have the car towed into the local dealer where the unit and keys need to be re-coded. This has happened to me twice in a year's time. Not only is this costly, incredibly inconvenient, but a safety hazard should it happen on a road trip. Honda refuses to do any accommodation or fix of this problem.
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all problems of the 2006 Honda Civic
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The Civic would start for a few seconds and then shut down. The anti-theft immobilizer indicator light came. All three oem keys did not work. This resulted in the need for a long distance tow to the Honda dealership, as well as $209 in repairs. I was told by the service department that the immobilizer module was bad and had to be replaced, along with suggesting a new battery. Keys failing to work??? come on Honda! of all things to go wrong with a car, this just shouldn't happen. On top of that you stick your customer's with a costly tow in the middle of the winter. What would have happened if I had been stuck in the middle of nowhere, stranded, simply due to my keys failing to work? it would appear your vaunted quality control is slipping the last few years. I noticed there was a "service bulletin" listed for this item, but no compensation forthcoming from Honda.