It's the largest civil penalty the agency has levied against an automaker.
Honda disclosed the reporting failure in November, admitting that company officials had waited three years after finding out about the reporting failure before making the disclosure to the National Highway Traffic Safety Administration.
Transportation Secretary Anthony Foxx said the government won't tolerate automakers withholding safety information. He said regulators had shared information about the case with the Justice Department. The private Center for Auto Safety has called for a criminal investigation into the case.