Workers have to agree in writing to last-minute schedule changes and employers must pay workers a premium for making these changes. Companies are also required to give workers the opportunity for additional hours instead of hiring more part-timers.

The law also requires companies to get consent and pay extra when they schedule employees for so-called clopenings, which require a worker to close a store then return early the next day to open it.

The city is also continuing to investigate complaints at 11 additional Chipotles in Manhattan, according to the commissioner for consumer and worker protection, Lorelei Salas.

“This is a very large corporation that should have known better — that does know better,” Ms. Salas said, “because this investigation has been going on since early 2018, and still, as of today, Chipotle has not fixed their practices.”

In a statement, Chipotle said it was working to address the city’s concerns.

“Chipotle has been working cooperatively with the city to ensure we have systems and processes in place to comply with the law, so we believe the filing of charges was unnecessary” said Laurie Schalow, Chipotle’s chief reputation officer.

Ms. Schalow added that Chipotle’s employees knew the company was committed to creating a “safe and engaging work environment” that was in compliance with all relevant laws and regulations. She said Chipotle encouraged its workers to contact the company immediately if they had concerns.

But Ms. Salas said Chipotle, which owns and operates more than 80 locations in New York City, only began to cooperate when the city threatened a lawsuit. She noted that her department was still receiving complaints.