A fault in the electric wiring between the handle switch and the headlights can cause the low beam to fail to light up, the company said.
No accident has been reported as a result of the defect, a Honda spokeswoman said, but the automaker had reported 130 cases of the defect to the Japanese transport ministry.
The Fit cars were built at Honda's Suzuka factory in Japan between November 2001 and October 2007.
About 385,000 units were shipped to Europe, and the model has also been exported to the United States, Asia, the Middle East and Africa, she said.