The fine imposed by the US National Highway Traffic Safety Administration (NHTSA) is the highest in US history for a single recall campaign over the June call-back of 154,000 2010 Lexus RX 350 and RX 450h vehicles, Detroit News said.
The latest recall came following NHTSA's investigation in May after it saw an increase in car consumer complaints, reported Xinhua.
Toyota told NHTSA in June it knew of 63 reports of possible floor mat pedal entrapment.
NHTSA sought an immediate recall for what it deemed a serious safety issue and then opened an investigation into Toyota's conduct.
It's the fourth time for Toyota to pay fines for delaying recalls since 2010.
In the year 2010, Toyota paid $48.8 million in civil penalties for failing to recall millions of vehicles in three separate campaigns.
Toyota says it will restructure its organization to consolidate responsibility for quality assurance and review of safety-related issues in the US, according to a draft five-page agreement between Toyota and the US government.
Ray Tanguay, chief quality officer of Toyota North America, said: "Toyota is dedicated to the safety of our customers, and we continue to strengthen our data collection and evaluation process to ensure we are prepared to take swift action to meet customers' needs. We agreed to this settlement in order to avoid a time-consuming dispute and to focus fully on our shared commitment with NHTSA to keep drivers safe."