Justice Department lawyers said on Wednesday that the government was taking steps to comply with a court order to facilitate the return of a man who had been deported to Mexico and was then sent to Guatemala.

The Guatemalan man, known by the initials O.C.G., had been deported this year despite having told U.S. authorities that he had experienced violence in Mexico and was afraid to go back.

Immigration authorities made contact with O.C.G.’s legal team over the weekend and were working to bring him back to the United States on a charter flight, according to the two-page filing in the case before Judge Brian E. Murphy of the Federal District Court in Massachusetts.

Late last week, Judge Murphy ordered the government to “facilitate” O.C.G.’s return to the United States, finding that he was likely to “succeed in showing that his removal lacked any semblance of due process.”

The government’s agreement to return O.C.G. represents a substantial de-escalation in a case that is shaping up to be one of the key courtroom battles over President Trump’s attempts to conduct mass deportations.

It also marks a departure from the more defiant stance that the administration has taken in other immigration matters, including the case of Kilmar Armando Abrego Garcia. Mr. Abrego Garcia was deported to El Salvador despite an order from an immigration court that he not be sent there, a mistake the government has called an “administrative error.”