“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,” said Assistant Attorney General Jody Hunt of the Justice Department’s civil division. “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 in a statement that Chipotle failed to “ensure that its employees both understood and complied with its food safety protocols, resulting in hundreds of customers across the country getting sick.”

“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,” Mr. Hanna said.

He added that it would “remind others in the industry to review and improve their own health and safety practices.”

Prosecutors said that the charges in the case “stem in part from incidents related to outbreaks of norovirus,” which spreads easily and can cause diarrhea, vomiting, nausea and stomach pain.