Barack Obama warned Donald Trump in November against hiring Michael Flynn, who was forced to resign as national security adviser over his contacts with Russia after less than three weeks in office.

The outgoing president issued the warning when the two men met in the White House two days after Trump’s election victory, White House spokesman Sean Spicer confirmed on Monday.

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Spicer acknowledged that Obama had expressed misgivings about Flynn, a former general, but said they were general criticisms.

“It’s true that President Obama made it known that he wasn’t exactly a fan of Gen Flynn’s,” Spicer said, but added that such remarks were unsurprising as Flynn had been an outspoken critic of the Obama administration’s policies. He said Flynn’s security clearance had been renewed in April 2016, and the Obama White House had not stepped in to revoke it.

Flynn was appointed head of the Defense Intelligence Agency (DIA) in 2012 but was fired two years later, reportedly over dissatisfaction over his management style and temperament. Reports on Monday attributed to Obama officials differed on whether the concerns voiced by Obama were linked to his DIA performance or because of his Russia links. Flynn had received income from RT in 2015, a state-run television channel formerly known as Russia Today, which he did not initially declare.

Despite Obama’s warnings, Trump picked Flynn as his national security adviser, but the retired general was forced to resign after little more than three weeks after it emerged he had had extensive contacts with the Russian ambassador to Washington, Sergey Kislyak, and had not given a full account of them to other White House officials.

Federal records also showed that his company, the Flynn Intel Group, had been paid more than a half-million dollars to lobby on behalf of projects that benefited the Turkish government in 2016.

The news reports that Obama had alerted Trump over concerns about Flynn came hours before the former acting attorney general Sally Yates was due to testify to a Senate committee on her own warnings to the White House days after Trump took office that Flynn had put himself in a compromising position by his failure to make a full disclosure of his Kislyak contacts. Yates was fired a few days after her White House warning, at the end of January, for refusing to defend the travel ban, suspending entry for refugees and travelers from seven Muslim countries, in court.

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Yates’ testimony is expected to contradict the White House, which has sought to play down the detail and severity of her warnings about Flynn, at a time when the Trump campaign’s contacts with the Russian government in general are under scrutiny by the FBI and Congress.

But in her written testimony, Yates told the committee she was limited in what she could say in open hearing.

“I want to note that I intend my answers today to be as fulsome and comprehensive as possible while respecting my legal and ethical boundaries,” she said. “As the subcommittee understands, many of the topics of interest today concern classified information that I cannot address in this public setting, either directly or indirectly. My duty to protect classified information applies just as much to me as a former official as it did when I led the department.”

On the day of her testimony, Trump tweeted: “Ask Sally Yates, under oath, if she knows how classified information got into the newspapers soon after she explained it to [White House] counsel.”

The tweet referred to a conversation Yates had with the White House legal adviser, Donald McGahn, about Flynn’s position, and appeared to hint that she would know who had leaked the content of the discussion.

Asked about the meaning of the message, Spicer said: “The tweet speaks for itself.”

Trump also blamed the Obama administration for giving Flynn a security clearance. “General Flynn was given the highest security clearance by the Obama Administration - but the Fake News seldom likes talking about that,” the president tweeted on Monday.

Spicer echoed this attack at his briefing, asking: “If President Obama was truly concerned about Flynn, why didn’t he pull his security clearance?”

CNN reported that the concerns Obama raised about Flynn when he met Trump at the White House were connected to the Russia investigation.

“Flynn’s name kept popping up,” one senior Obama administration source is quoted as saying.

However, NBC quoted a former official as saying that Obama had only passed on “a general caution that he believed Flynn was not suitable for such a high-level post”.

Retired military officers can retain their security clearance subject to periodic background checks, which cover foreign payments and contacts. Failure to make full disclosure of such contacts in an application for renewal of clearance is punishable by a fine or five years imprisonment.

Obama administration officials say that such security clearance renewals after retirement are routine, and that vetting for a top White House post such as national security adviser would require a much higher threshold. They said such vetting was the responsibility of any incoming administration.

Additional reporting by Ben Jacobs in Washington