The US Department of State’s top official for Latin America has resigned, reportedly amid disputes over immigration policy.

The state department did not comment on the departure of Kimberly Breier, a former CIA analyst and an expert on Mexico, but it was confirmed by Ivanka Trump on Twitter. Breier then replied thanking the president’s daughter and her husband, Jared Kushner, for their “friendship and support”.

Several reports said Breier’s resignation from the post of assistant secretary of state for the western hemisphere followed a heated internal dispute over an agreement with Guatemala at the end of July, requiring Central American immigrants to seek asylum in that country before coming to the US.

The accord designated Guatemala a “safe” country able to process asylum claims and accommodate migrants fleeing poverty, violence and climate change from the region.

The state department, including the secretary of state, Mike Pompeo, is reported to have vigorously opposed the deal, on the grounds that Guatemala, plagued by the same problems as its neighbours, was in no state to honour the agreement.

But the agreement was forced through by Trump and immigration hardliners in the White House and the Department of Homeland Security (DHS).

According to the Washington Post, which first reported the resignation, Breier was chastised in an internal administration email chain by Stephen Miller, Trump’s far-right policy adviser, for being half-hearted in defending the Guatemala agreement, saying it was “her job” to do so.

Mortan Ortagus, the state department’s spokeswoman, said Breier had resigned for family reasons. She denied the Guatemala agreement was a factor in the decision.

“She’s addressed that with me directly,” Ortagus told journalists. “And she said there’s absolutely no truth to that. The Washington Post reported that there was an email from Stephen Miller. She’s denied ever seeing this email.”

Breier, aged 46, served as a Latin America adviser in the George W Bush administration after her time as a CIA analyst, and is widely seen as a moderate Republican and pragmatist. She drew broad support at her Senate confirmation hearings last year.

“I do think it’s a loss,” said Mark Feierstein, a senior director for western hemisphere affairs in the Obama White House. “American policy is largely being driven now in this administration by ideologues who don’t know the region very well and she’s someone who’s pragmatic, experienced, and level-headed.”

Feierstein said he had not spoken to Breier personally and so could not confirm her motives for resigning, but added: “Anybody who knows anything about Guatemala and about migration recognises that the idea is that Guatemala would be some sort of a safe place for people from other countries to request asylum is just preposterous.

“Kim obviously knows that Guatemala is a poor and unsafe country as it is. They are in no position whatsoever to be accepting people requesting asylum rights.”

Breier’s resignation is the fourth departure of an assistant secretary of state so far this year, in an administration in a constant state of turmoil over policy and turf wars.

Chuck Park, a foreign service officer, announced his own resignation in the Washington Post on Thursday, saying it was impossible to continue to serve what he called “Trump’s toxic agenda”.

He said the department did not represent the “deep state” but the “complacent state” which “sighs when the president blocks travel by Muslim immigrants; shakes its head when he defends Saudi Crown Prince Mohammed bin Salman; averts its gaze from images of children in detention camps. Then it complies with orders.”

“I’m ashamed of how long it took me to make this decision,” Park wrote. “My excuse might be disappointing, if familiar to many of my colleagues: I let career perks silence my conscience. I let free housing, the countdown to a pension and the prestige of representing a powerful nation overseas distract me from ideals that once seemed so clear to me. I can’t do that anymore.”

On a particularly turbulent day for the state department, it was also reported that it had suspended an employee in its energy bureau, after allegations he had been an active member of a white supremacist group for more than five years.