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Geoffrey Berman, the federal prosecutor ousted over the weekend by the Trump administration, recently refused to sign a letter from the Justice Department that criticized New York City’s coronavirus restrictions that affect religious institutions, a person briefed on the matter said.

Attorney General William Barr wasn’t aware of the dispute, and it had nothing to do with the ouster of Berman, the person said. The letter was sent Friday from the Justice Department.

As CNN has reported, tensions between Berman and Barr, and other officials at Justice headquarters in Washington, had built over the years and they had planned last year to remove him before backing off when the investigation into Rudy Giuliani’s associates became public.

Berman’s refusal to sign the letter was first reported by The Wall Street Journal.

Two Justice Department officials overseeing state and local coronavirus policies accused New York City Mayor Bill de Blasio as having previously “demonstrated a troubling preference for certain First Amendment rights over others” in a statement Monday, while expressing approval that the city was opening houses of worship to 25% indoor capacity under Phase 2 of reopening.

“Mayor de Blasio’s recent public statements and enforcement of COVID-19 Orders have demonstrated a troubling preference for certain First Amendment rights over others,” said Assistant Attorney General for Civil Rights Eric Dreiband and US Attorney for the Eastern District of Michigan Matthew Schneider.

They added, “The Justice Department is glad Mayor de Blasio will now permit greater religious exercise and will continue to monitor New York City’s reopening to ensure that New York City extends the same respect to the freedom of religion, both in terms of indoor and outdoor gatherings, as it does to the freedoms of speech and assembly.”

Berman’s departure came a day after he refused Barr’s request that he resign. In a curt letter to Berman on Saturday, Barr told him President Donald Trump had agreed to remove him and conceded that Berman’s deputy would succeed him.

“Unfortunately, with your statement of last night, you have chosen public spectacle over public service,” Barr wrote in his letter to Berman. “Because you have declared that you have no intention of resigning, I have asked the President to remove you as of today, and he has done so.”

He provided no justification for pushing out Berman.

Though Barr had said Friday that he would install Craig Carpenito – who is close to Barr and is now the US attorney in New Jersey – to serve as Berman’s acting replacement, the attorney general’s letter Saturday noted that “by operation of law,” Berman’s current deputy, Audrey Strauss, will become acting US attorney.

“I anticipate that she will serve in that capacity until a permanent successor is in place,” Barr wrote.

Though it isn’t clear that any one particular investigation or conflict led to Berman’s ouster, federal prosecutors in New York, working under Berman, have continued to pursue cases that pose significant threats to Trump and his allies. In the past month, according to two people familiar with the matter, prosecutors and FBI agents have been interviewing witnesses as part of their investigation concerning Giuliani and associates Lev Parnas and Igor Fruman.

Senate Minority Leader Chuck Schumer, a New York Democrat, on Monday sent a letter to Justice Department Inspector General Michael Horowitz and Office of Professional Responsibility Director Jeffrey Ragsdale requesting a joint investigation into Berman’s firing. House Judiciary Chairman Jerry Nadler, another New York Democrat, on Sunday said during an interview with CNN’s Jake Tapper that he is confident Berman will testify before his committee.

Last month, Trump deemed houses of worship “essential” during the coronavirus pandemic and urged governors to reopen them for services.

According to the latest guidance from the US Centers for Disease Control and Prevention, religious institutions are advised to encourage congregants and staff to frequently wash their hands, use hand sanitizer and wear face coverings.

This story has been updated with additional background information.

CNN’s Erica Orden, Manu Raju, Kara Scannell and Chandelis Duster contributed to this report.