NORTHAMPTON — The city agreed Tuesday to rescind a stop-work order preventing the Roman Catholic Diocese of Springfield from removing five stained-glass windows at St. Mary of the Assumption Church, a negotiated settlement made three days after a judge implored the two sides to figure it out before he ruled.

The settlement calls for the diocese to drop its federal lawsuit against the city in exchange for the lifting of the stop-work order for the long-shuttered church on Elm Street.

The diocese filed the lawsuit in U.S. District Court earlier this year objecting to the stop-work order.

The windows are located above the church’s altar and considered by the church to be “sacred objects” that depict several scenes from the Bible. The diocese wants to remove the windows ahead of an impending sale of the building to an Amherst developer.

As an additional part of the agreement, the diocese agreed to repair any damage that was caused to the exterior protection glass on the five contested windows.

The city ordered a halt to the work because the church falls within the Elm Street Historic District, and requires a special permit before work can be done.

“The diocese is grateful to the court for its guidance in this matter and we look forward to working cooperatively with the City of Northampton to finalize work needed in advance of the sale of this property and its planned redevelopment,” said Carolee McGrath, the media relations manager, in a statement.

To that end, the diocese said it has already filed a permit to remove the windows, according to the statement.

Northampton city officials did not respond to a request for comment on the settlement as of 3 p.m. Thursday.

The settlement decision comes after both sides were urged by federal judge Mark Mastroianni to reach an agreement, during an evidentiary hearing in the case that occurred in Springfield on Monday. Mastroianni said there was no reason why the church and the city could not reach a good faith agreement over the removal of the windows.

Mastroianni also called the condition of the closed church “pathetically sad,” with signs of homeless encampment and syringes present inside the church — issues that both church and city officials have pledged to address.

The settlement means a ruling on the case, scheduled for Thursday, did not take place.

McGrath said earlier this month that the diocese intends to make the windows available elsewhere, as was the case with the church’s marble altar, which was given to a chapel at Christendom College, a Catholic college in Virginia.

St. Mary of the Assumption Church has been closed since 2010. The diocese had entered into a purchase and sale agreement to transfer the property to Sunwood Builders of Amherst, known for several housing developments around the Pioneer Valley. According to its website, Sunwood specializes in “building distinctive luxury homes” that are “architecturally suited” for the region.

Alexander MacDougall can be reached at amacdougall@gazettenet.com.