In one sign that Mr. Barr’s move to oust Mr. Berman may have been hastily arranged, even Mr. Clayton, the man who had been poised to take Mr. Berman’s place, appeared to be caught off guard.
Mr. Clayton had sent an email to his staff on Thursday saying that he looked forward to seeing them in person, once work-at-home restrictions that had been put in place because of the coronavirus could be lifted. The email offered no indication that Mr. Clayton was planning to leave the S.E.C., according to a person briefed on it.
Just after midnight on Saturday, Mr. Clayton sent another email to his employees, telling them about his new position. “Pending confirmation,” he wrote, “I will remain fully committed to the work of the commission and the supportive community we have built,” according to a copy reviewed by The New York Times.
Mr. Clayton could not be reached for comment.
On Saturday, Representative Jerrold Nadler, a New York Democrat who heads the House Judiciary Committee, said the committee would investigate the firing of Mr. Berman as part of a larger inquiry into what he said was undue political interference at the Justice Department.
“The whole thing smacks of corruption and incompetence,” Mr. Nadler said of Mr. Berman’s dismissal.
Under Mr. Trump, the Justice Department has long believed that the Southern District was out of control. In no small part that was because the department believed that prosecutors in New York delayed in warning them that they were naming Mr. Trump — as “Individual-1” — in court documents in the Cohen prosecution.
When Mr. Barr became attorney general, officials in the deputy attorney general’s office, which oversees regional prosecutors, asked him to rein in Mr. Berman, who they believed was exacerbating the Southern District’s propensity for autonomy. The office has embraced its nickname the “Sovereign District” of New York because of its tradition of independence.
One particular point of contention was the question of how Mr. Berman and his staff should investigate Halkbank, a Turkish state-owned bank that the office indicted last year, according to three people familiar with the investigation.