This month, the department took the unusual step of asking a federal judge to enforce the accord over the district's objections.
District officials have not answered the government's request in court. A spokeswoman did not respond to questions about why the school system did not want the deal made public.
But Justice Department lawyers say that they never negotiate confidential settlements and that the district knew that from the start of negotiations.
School officials have hardly shied away from publicity surrounding civil rights settlements in the past.
Former school Superintendent Arlene C. Ackerman publicly endorsed a 2010 agreement with the federal government monitors aimed at protecting Asian students at South Philadelphia High from racial bias. That accord, she said at the time at a School Reform Commission meeting, recognized "lessons learned."
This time, though, attitudes appear to have changed.
The suit at the center of the current dispute was filed in March by Siddiq Abu-Bakr, a police officer who has worked for the district since 1987. He contended that his civil rights were violated when he was ordered to trim his beard to a quarter-inch length under a dress-and-grooming code adopted by the district in 2010.
Abu-Bakr, who has maintained a long beard for religious reasons throughout his employment with the district, refused, and was reprimanded and threatened with further disciplinary action. His suit sought a religious accommodation to the dress code and monetary damages for any other affected district employees.
Court filings suggest the district and Justice Department attorneys reached an agreement within months of the filing of Abu-Bakr's suit. The school system would revise its grooming code to allow for religious accommodations and provide supervisor training.
Two officers would be offered $4,500 in monetary damages. Abu-Bakr has settled his claims with the district separately for an unspecified sum, according to court filings.
E-mails traded between the parties suggested the deal was all but done by July 2.
"The modified agreement looks fine," School District lawyer Talib Ellison wrote in an e-mail that day. "We should be good to go with wrapping that up."
Hours later, the Justice Department says, the district returned with an ultimatum: Keep the deal off public court dockets, or it would back out.
U.S. Magistrate Judge David Strawbridge, who is handling the case, has not yet set a hearing to discuss the Justice Department's request.