Customs and Border Protection commander-at-large Greg Bovino is returning to El Centro, California, to resume his duties as chief of that sector, multiple sources told ABC News.

The position of commander-at-large was a temporary position. 

Dept. of Homeland Security assistant secretary Tricia McLaughlin said in a statement on Monday that Bovino “has NOT been relieved of his duties,” referring to him as a “key part of the President’s team and a great American.”

It comes as Bovino and some Border Patrol agents are leaving Minneapolis, just as Border Czar Tom Homan arrives in the city.

President Donald Trump on Monday announced he is dispatching Homan — bypassing the normal chain of command — where Homeland Security Secretary Kristi Noem and Bovino have been overseeing ICE operations.

“He has not been involved in that area, but knows and likes many of the people there. Tom is tough but fair, and will report directly to me,” Trump wrote in a social media post.

Noem and Chief Advisor Corey Lewandowski met with Trump for almost two hours on Monday, according to the New York Times.

It was at her request, according to the Times, and her job reportedly isn’t in jeopardy.  

Tensions over the administration’s sweeping immigration enforcement escalated over the weekend after the federal agent-involved deadly shooting of Alex Pretti in Minneapolis on Saturday.

Multiple videos of the confrontation Saturday showed federal agents spraying Pretti with pepper spray and pinning him to the ground before the shooting.

The Department of Homeland Security alleged that Pretti approached Border Patrol agents with a 9mm semi-automatic handgun, and “violently resisted” when agents tried to disarm him. Local officials have disputed that characterization.

It marked the second fatal, federal agent-involved shooting in Minneapolis this month.

Noem, Bovino and FBI Director Kash Patel have defended the agents’ actions. Noem said Pretti had been “brandishing” a gun and possessed multiple magazines with the intent to inflict harm on officers — a “massacre,” Bovino claimed. Patel went so far as to suggest carrying a gun to a protest is illegal.

State and local officials said Pretti was lawfully carrying a gun, with a concealed carry permit, and video reviewed and verified by ABC News does not appear to show that Pretti drew his gun on the agents and instead was holding up a cell phone, not a gun, to record agents during the incident.