The commissioner, Chris Magnus, has refused to step down amid criticism over his agency’s lack of accountability.
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Chris Magnus oversees much of the customs and trade policy, as well as the country’s borders.
WASHINGTON — The Customs and Border Protection commissioner said Friday that he had been asked to step down but was refusing to do so, in what appears to be the Biden administration’s first attempted shake-up after the midterm elections.
The commissioner, Chris Magnus, who oversees much of the customs and trade policy and the country’s borders, said both Alejandro N. Mayorkas, the homeland security secretary, and the department’s deputy secretary asked him to resign or face being the first political appointee to be fired by President Biden. Mr. Magnus has been in the position for less than a year.
In a statement, Mr. Magnus said, “I have no plans to resign as C.B.P. commissioner,” according to a copy he shared with The New York Times.
Mr. Magnus, 62, plans to go to work on Monday, he said. He added that the department already cut off his access to its Twitter account.
The Homeland Security Department declined to comment.
Mr. Biden tapped Mr. Magnus, a former police chief, to run Customs and Border Protection, one of the largest law enforcement agencies in the world that has long been criticized for its lack of accountability. He is also the first openly gay commissioner of C.B.P.
Mr. Magnus said he was told that Mr. Mayorkas had lost confidence in him and that the president will support Mr. Mayorkas. Some officials have said Mr. Magnus is not engaged enough in the job and not doing enough to address the high number of illegal border crossings.
Just a few months into the Biden administration, the number of illegal crossings at the southwestern border started to increase, and they have since broken records, drawing relentless Republican criticism.
It is a situation that has weighed heavily on the White House as a political vulnerability, even during a time when there are more displaced people around the world than ever before. Many who come to the United States by crossing the border illegally are fleeing violence and political instability.
House Republicans have said they plan to impeach Mr. Mayorkas if they take control of the House. They blame him for what they see as a lack of control at the southwestern border.
Mr. Mayorkas is scheduled to appear before several congressional committees next week.