The $25 million fine was the largest levied in a food safety case, the Justice Department said.
"This case highlights why it is important for restaurants and members of the food services industry to ensure that managers and employees consistently follow food safety policies," Assistant Attorney General Jody Hunt, of the Department of Justice's Civil Division, said in the news release. "The Department of Justice will vigorously enforce food safety laws in order to protect public health."
Nick Hanna, U.S. attorney for the Central District of California, said Chipotle failed to ensure its workers understood and complied with food safety protocols.
"Today's steep penalty, coupled with the tens of millions of dollars Chipotle already has spent to upgrade its food safety program since 2015, should result in greater protections for Chipotle customers and remind others in the industry to review and improve their own health and safety practices," Hanna said in the news release.