It sounds like your Honda Civic Hybrid has not yet completed the drive cycle. Usually driving in both city and highway conditions over the course of a few days is enough to get the drive cycle to run and set the monitors. At times however, due to individual driving habits, following a Honda Civic Hybrid drive cycle is required.
Follow the drive cycle carefully. Take extra caution when performing the drive cycle on public roadways. If you feel you will be unable to follow the drive cycle safely, please seek assistance from an smog check repair station or Honda service center. They may be able to perform the drive cycle utilizing a dynamometer, and specialized scan tools. Perform the drive cycle at your own risk.
Prior to beginning the drive cycle ensure your vehicle has between 15% to 85% fuel in the gas tank, and that the engine is cold. It is best to start the driving cycle after your Honda has been parked overnight for at least 6 hours. Ambient temperature should be between 40° and 95°F
Honda Civic Hybrid Drive Cycle
A. Start the engine and without touching the accelerator pedal allow it to idle for 20 seconds.
B. Increase the engine speed to 2,000 rpm and hold RPM for three minutes until engine warms up. Temperature gauge should indicate normal operating temperature. Keep gas pedal steady and transmission in park.
C. Begin driving. Place transmission in Drive and speed up to 50-60 miles per hours. Maintain this speed for at least 20 minutes. Do not use cruise control. This step should be performed on the highway.
D. Drive for 90 seconds without moving the accelerator pedal.
E. Drive the vehicle in city traffic for at least 10 minutes.
F. Coast down several seconds without touching the accelerator pedal or the brake pedal.
G. Stop vehicle and turn engine off. Allow while to remain parked for 30 minutes.
H. Check the monitors. The best way to do this is via a Scan Tool. If a scan tool is not available you may use the system's onboard monitor check as follows: Turn ignition switch to the ON position. Do not start engine. Monitor the Malfunction Indicator Lamp (MIL). The MIL will illuminate for 20 seconds. If it turns off, this is an indication that the monitors are ready. If the MIL blinks five times, the readiness monitors are not ready and you should perform the drive cycle again, assuming the vehicle has no emission related issues.