The charges related to "adulterated food that sickened more than 1,100 people across the United States from 2015 to 2018," the department said in a release.
The fine is the largest "ever imposed in a food-safety case," the department said.
"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," said United States Attorney Nick Hanna.
The restaurant chain also agreed to put in place a "comprehensive food safety compliance program," the department said.
Chipotle said it has "introduced specific food safety policies and procedures to enhance its existing practices."
"This settlement represents an acknowledgment of how seriously Chipotle takes food safety every day and is an opportunity to definitively turn the page on past events and focus on serving our customers real food made with real ingredients that they can enjoy with confidence," Chipotle Chairman and CEO Brian Niccol said in a statement.
The Justice Department said the charges stemmed from cases of norovirus, a "highly contagious pathogen that can be easily transmitted by infected food workers handling ready-to-eat foods and their ingredients."
There were at least five food-safety incidents at Chipotle restaurants around the country between 2015 and 2018, the department said, describing cases where employees continued to work at various locations, even though they were sick.
Chipotle said it has "introduced specific food safety policies and procedures to enhance its existing practices."
"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, of the Justice Department, said.
CNN has requested additional comment from Chipotle.