Kirstjen Nielsen, the homeland security secretary who has been the public face of some of the Trump administration’s most contentious policies, has resigned.

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In a tweet on Sunday, Donald Trump said: “Secretary of Homeland Security Kirstjen Nielsen will be leaving her position, and I would like to thank her for her service.

“I am pleased to announce that Kevin McAleenan, the current US Customs and Border Protection Commissioner, will become Acting Secretary. I have confidence that Kevin will do a great job!”

In a tweet late on Sunday, Nielsen said that she would stay on until Wednesday “to assist with an orderly transition”.

Nielsen’s position had been rocky for some time. In November, leaks from the White House suggested she would be out by the end of the year as Trump fulminated against what he complained was her weak performance.

The previous May, the New York Times reported that Trump had humiliated her in front of the entire cabinet, castigating her for failing to reduce the numbers of undocumented migrants entering the US from Mexico. The newspaper said she considered quitting then.

But in the end she managed to hang on for a little more than a year, having taken up the job in December 2017 on the recommendation of her predecessor, Gen John Kelly, who became Trump’s second chief of staff. He left the administration three months ago.

In office, Nielsen had to defend several of Trump’s most controversial policies, including his increasingly eccentric demands for a border wall, which caused a 35-day government shutdown, his declaration of a national emergency to access funds for the wall, and last summer’s family separations at the border which led to accusations of cruelty around the world.

In late March, McAleenan made a dramatic intervention in the public debate about the surge in Central American asylum seekers at the southern border with Mexico, saying the system had reached “breaking point”. On Friday, Nielsen accompanied Trump to the border.

“There is indeed an emergency on our southern border,” Trump said then, in California. “It’s a colossal surge, and it’s overwhelming our immigration system. We can’t take you any more. Our country is full.”

Play Video 0:38 Trump says the US is 'full' on visit to US-Mexico border – video

According to CBS News, which first reported the news of Nielsen’s impending resignation, her departure is yet another victory for Stephen Miller, the far-right senior adviser in the White House who has consistently steered the president in a hardline direction on immigration.

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The extreme hand of Miller was also seen behind Trump’s sudden announcement on Friday that he had withdrawn his nominee as new director of US Immigration and Customs Enforcement (Ice). Trump said he was pulling Ronald Vitiello as “we want to go in a tougher direction”.

Nielsen’s departure adds to the lightning speed with which cabinet members and other senior officials have come and gone within Trump’s turbulent government. Seventeen senior administration figures have departed so far and the key roles of secretary of defense, secretary of the interior, homeland security secretary, White House chief of staff and ambassador to the United Nations are currently filled in an acting capacity.

Trump has said he likes having people “acting” in key roles as it gives him “more flexibility” but critics have questioned the constitutionality of the practice.

The removal of Nielsen further skews the composition of Trump’s cabinet in a hyper-male direction, with the resignation of Linda McMahon, announced in March, to take effect this week. Of the cabinet members remaining, only three are women: Gina Haspel as CIA director; Betsy DeVos as education secretary; and Elaine Chao in charge of transportation.

Nielsen had a very rough ride as the fall guy for Trump’s hardline immigration policy. But given the controversial policies that she consistently championed, there were few expressions of sorrow for her on Sunday night.

A former DHS senior official, Juliette Kayyem, tweeted: “Nielsen is without an agency, and Administration, and public sympathy.”

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Ronald Newman, political director of the American Civil Liberties Union, charged Nielsen with allowing the DHS to act as the “key cog in Trump’s unconstitutional and anti-immigrant agenda of fear”. He accused her of overseeing “gross civil rights and civil liberties violations that will go down as among the worst failures in Trump’s chaotic presidency”.

Nielsen’s failures, Newman said, ranged from “the family separation crisis she created and defended, to the restricting of immigrants’ rights to seek asylum, to the relentless yet pointless efforts to build Trump’s border wall”.

It emerged on Saturday that the Trump administration has predicted it could take two years to identify all families affected by the separations policy. Nielsen memorably and repeatedly claimed no such policy existed.

In her resignation letter, Nielsen continued to press the line that she had adopted in post over several months: that Congress and federal judges, not Trump, were responsible for the rising mayhem at the border.

She wrote: “Despite our progress in reforming homeland security for a new age, I have determined that it is the right time for me to step aside. I hope that the next secretary will have the support of Congress and the courts in fixing the laws which have impeded our ability to fully secure America’s borders and which have contributed to discord in our nation’s discourse.”