Kevin McAleenan Resigns as Acting Homeland Security Secretary

“I also believe strongly in investing in the growing collaboration with the governments of Guatemala, El Salvador and Honduras, and see real opportunity to change the dynamic in the region through these partnerships,” Mr. McAleenan said in his resignation letter.

While Mr. McAleenan had the strong backing of Jared Kushner, the president’s son-in-law and senior adviser, he clashed over personnel decisions with Stephen Miller, a White House aid and the architect of Mr. Trump’s immigration agenda. In recent months, Mr. McAleenan grew increasingly irritated by the harsh language used by agency officials installed by the White House.

Kenneth T. Cuccinelli II, who once advocated an end to birthright citizenship, was installed to lead the agency that manages legal immigration. Mark Morgan, who once said he could determine future gang members by looking at detained migrant children, was selected to oversee Immigration and Customs Enforcement. He then replaced John Sanders, an ally of Mr. McAleenan, to lead Customs and Border Protection. Both are serving in acting positions.

None of those hard-liners can immediately succeed Mr. McAleenan under the Vacancies Act, which stipulates that the position must go to certain ranked officials in the department. Mr. Cuccinelli would face strong opposition from the Senate majority leader, Mitch McConnell of Kentucky, for his political efforts to back insurgent Senate candidates, including one challenging Mr. McConnell.

Bennie Thompson, the chairman of the House Homeland Security committee, derided the department’s turnover. “President Trump cannot continue to rely on instilling ‘acting’ — and potentially unlawful — figureheads for this critical position,” Mr. Thompson said in a statement. “The next secretary must also understand that bowing to President Trump’s obsession over a wall and keeping people out is not part of the job description.”

Mr. McAleenan, a former lawyer who attended Amherst College, had pushed back on some of the White House’s initiatives. When Mr. Morgan and advocated widespread deportations to round up families that recently crossed the border, Mr. McAleenan delayed the operation for fear that families would be separated in the interior of the country and agents’ safety would be at risk.

When Mr. Trump threatened Mexico with tariffs this spring, Mr. McAleenan helped secure a deal that deployed Mexico’s military to its southern border to halt migration to the United States.

While homeland security grappled with the highest number of crossings at the southwestern border in more than a decade in May, the figures have declined by more than 65 percent. Along the way, migrants forced to wait in Mexico have been subjected to kidnappings and violence.