Earlier in her government career, Breier, who holds degrees in Spanish and Latin American studies, also handled regional issues as a CIA analyst and at the National Security Council under president George W. Bush. Immediately before becoming assistant secretary, she handled Latin American issues in the department’s policy planning office.

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Breier, 46, referred questions about her status to the State Department press office, which declined to comment. Several senior administration officials discussed the matter on the condition of anonymity because it concerns personnel.

She is the latest in a steady turnover at the assistant secretary level. Although Pompeo has filled many of the jobs left vacant by his predecessor, Rex Tillerson, a number are still held by acting officials, and at least four have departed this year, including A. Wess Mitchell, the top diplomat in charge of European affairs.

In May, Yleem Poblete, assistant secretary for arms control verification and compliance and a prominent Iran hawk, resigned. Poblete’s views were reportedly more aligned with those of White House national security adviser John Bolton than her direct supervisor at the State Department. Earlier this month, Kiron Skinner, who headed the State Department office of policy planning, was forced out of her job over personnel clashes.

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Officials said Breier, a Mexico expert, was not necessarily opposed to administration policies in the region but chafed at the level of control exerted by the White House over immigration and trade-dominated relations with Mexico and other matters.

One senior administration official said she had been chastised, in a particularly unpleasant recent email chain, by White House policy adviser Stephen Miller, who considered her insufficiently committed to publicly defending last month’s sudden agreement over asylum between President Trump and the government of Guatemala.

The safe third country agreement requires Central American migrants to seek asylum in Guatemala and be rejected there before the United States will consider their asylum requests here. Pompeo reportedly objected to the White House-negotiated deal on grounds that Guatemala, one of the world’s most violent countries, was not equipped to provide secure refuge for migrants fleeing Honduras and El Salvador.

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Others in the department, some of whom have circulated for signatures a dissent channel memo on the subject, have also objected to it on the grounds that it violates U.S. asylum law.

Miller, the senior official said, pointed out to Breier that Trump had stood behind Kevin ­McAleenan, the acting secretary of homeland security, and Guatemala’s interior minister when they signed the deal and that it was “her job” to defend it.

Another senior official, however, sharply pushed back on that version of events and denied the email exchange existed. Among a number of officials who criticized or praised Breier, only one would go on the record.

Ivanka Trump, on Twitter, said, “Thank you @WHAAsstSecty Kim Breier, for your friendship and great service.” Posting a photograph of herself with Breier and Breier’s daughter, Emma, Trump said that she and her husband, White House adviser Jared Kushner, “will miss working with you” but that “we are happy that Emma will now get to see more of the mom she is so proud of.”

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It was not clear whether the Guatemala issue was a principal cause a principal cause of Breier’s resignation. Other officials said Pompeo did not try to persuade her to stay.

Breier has been known at State as strongly protective of what she saw as her prerogatives, according to a number of officials who have worked with her.

In Latin America, Pompeo appointed a special envoy, Elliott Abrams, to lead diplomatic efforts on Venezuela, the biggest regional issue alongside immigration. Bolton and his senior director for the region, Mauricio Claver-Carone, have also played a significant public role in regional policy.