One problem related to engine clicking and tapping noises has been reported for the 2006 Honda Civic Hybrid. The most recently reported issues are listed below. Please also check out the statistics and reliability analysis of the 2006 Honda Civic Hybrid based on all problems reported for the 2006 Civic Hybrid.
Last year I had to have the catalytic converter replaced due to failure and at that time I informed the Honda dealer service technician hat the rpm's on the car were staying high even when the car was idle. The service tech said they checked the vehicle and could not replicate the issue and said they found nothing wrong with it. Now here we are 16000 miles later and I have a transmission failure. The car makes a clicking noise while in gear no other symptoms at this point. I have taken it to the dealer and they are aware of the failure, but are only willing to help me with 25% of the bill because I performed my own transmission fluid change and the warranty is up. This is the third problem I have had with the car in the three years I have had it.