It's the largest fine allowed under law for a single investigation.
Toyota's troubles stem from a 2012 recall involving one its Lexus models.
The NTSB says the automaker did not report a safety defect related to its floor mats in the Lexus RX 350 crossover in a timely manner.
The faulty floor mats could have trapped the vehicle's accelerator pedal, causing unwanted acceleration.
Toyota once had one of the best reputations for vehicle quality and safety.
But the company has been dogged by significant recall problems over the last three years.
It's already recalled more than 10 million vehicles worldwide for various problems so far this year.