Three days after his now infamous phone conversation with Ukrainian president Volodymyr Zelenskiy, Donald Trump abruptly fired his director of national intelligence in favour of an inexperienced political loyalist.

According to a New York Times report, the White House learned within days that the unorthodox call on 25 July with Zelenskiy had raised red flags among intelligence professionals and was likely to trigger an official complaint.

That timeline has raised new questions over the timing of the Trump’s dismissal by tweet of the director of national intelligence (DNI), Dan Coats, on 28 July and his insistence that the deputy DNI, Sue Gordon, a career intelligence professional, did not step into the role, even in an acting capacity.

Instead, Trump tried to install a Republican congressman, John Ratcliffe, who had minimal national security credentials but had been a fierce defender of the president in Congress. Trump had to drop the nomination after it emerged that Ratcliffe had exaggerated his national security credentials in his biography, wrongly claiming he had conducted prosecutions in terrorist financing cases.

Despite the collapse of the Ratcliffe nomination, Gordon was forced out. She was reported to have been holding a meeting on election security on 8 August when Coats interrupted to convince her that she would have to resign.

In a terse handwritten note to the president, Gordon said: “I offer this letter as an act of respect and patriotism, not preference. You should have your team.”

The Office of the DNI (ODNI) and its inspector general has the authority to receive whistleblower complaints from across all US intelligence agencies and determine whether they should be referred to Congress.

“We all knew Coats’ departure was coming because he had clashed with the president on several issues. What was weird was the president’s forcefulness in not wanting Sue Gordon to take over as acting director,” said Katrina Mulligan, a former official who worked in the ODNI, the national security council, and the justice department.

“I was hearing at the time that Sue was getting actively excluded from things by the president that she would ordinarily have taken part in, and she was being made to feel uncomfortable,” said Mulligan, now managing director for national security and international policy at the Center for American Progress.

“And then the president tried to install someone who was clearly unqualified,” she added. “Now the timeline of the whistleblower in the White House raises a lot of questions about the Sue Gordon piece of this.”

John McLaughlin, the former acting CIA director, said the fact that Ratcliffe’s nomination was dropped and the job of acting DNI ultimately went to an intelligence professional, Joseph Maguire, was a sign that the intelligence community was so far resisting political pressure from the White House.

Maguire faced tough questioning in Congress this week about his initial refusal, on justice department guidance, to refer the whistleblower complaint to Congress.

“On politicisation, my sense is that the community is holding the line against it although undoubtedly dealing with more or less constant pressure,” McLaughlin said. “I felt kind of bad for the acting DNI, an honourable man with impeccable service to the nation. I believe he made some honest errors in judgment rather than yielding to political pressure. Throwing him into this job in these circumstances on such short notice is a little like assigning me on a navy Seal mission.”