John Rood, the Pentagon’s top policy official who reportedly raised concerns about the freeze on military aid to Ukraine last year – the issue at the heart of Donald Trump’s impeachment – has resigned at the request of the president.

The Trump administration’s delay in releasing that aid was central to the president’s impeachment by the House on charges of abuse of power and obstruction of Congress. The Senate voted to acquit the president. But in the wake of the Senate trial, an emboldened Trump has gone after officials he has perceived as being disloyal.

Rood, the undersecretary of defense for policy, appears to be the latest official to be purged. He had certified last year that the defense department had seen enough anti-corruption progress in Ukraine to justify releasing congressionally authorized aid.

Earlier this month, the Trump administration also fired Gordon Sondland, the ambassador to the EU, and Lt Col Alexander Vindman from his White House post, who both delivered testimony deemed damaging to Trump during the impeachment inquiry.

At the time, Vindman’s lawyer, David Pressman, said: “He followed orders, he obeyed his oath, and he served his country. And for that, the most powerful man in the world – buoyed by the silent, the pliable and the complicit – has decided to exact revenge.”

Rood’s letter of resignation did not mention Ukraine but said that he was leaving at Trump’s request.

“It’s my understanding from Secretary Esper that you requested my resignation,” Rood said in his letter to Trump, adding that he will step down as of 28 February.

Mark Esper, the defense secretary, said Rood had played “a critical role’’ on issues such as nuclear deterrence, Nato, missile defense and the National Defense Strategy.

Trump tweeted on Wednesday that he wanted to “thank John Rood for his service to our Country, and wish him well in his future endeavors!”

Rood wrote in a 23 May letter to Congress that the Pentagon had made a thorough assessment of Ukraine’s anti-corruption actions and other reforms. And he said: “I have certified that the government of Ukraine has taken substantial actions to make defense institutional reforms for the purpose of decreasing corruption and making other improvements.”

Rood wrote that his certification, legally required before the aid could be released, was based on insights gained in “persistent US engagement” with Ukraine, including meetings between the US defense secretary and his Ukrainian counterpart.

He later told reporters: “In the weeks after signing the certification I did become aware that the aid had been held. I never received a very clear explanation other than there were concerns about corruption in Ukraine.”

He also spoke in favor of releasing the aid, suggesting that withholding it would hurt America’s defense priorities.

The Pentagon press secretary, Alyssa Farah, said James Anderson, who is currently serving as the deputy for policy, will take over the job until a permanent replacement is named by Trump and confirmed.

Associated Press contributed to this report