Flynn was left with nowhere to turn after being caught out – he lied to Vice-President Mike Pence, insisting that he had not discussed the Obama administration's sanctions on Moscow with Russian ambassador Sergey Kislyak in late December, prompting Pence to defend him publicly.

But US intelligence had monitored Flynn's call and provided a transcript to the White House.

It was a final bittersweet moment in an ugly and escalating war between Flynn and the combined US intelligence agencies. Flynn, and his boss the President, have repeatedly taunted the agencies as incompetent - but on Monday those same agencies were probably patting themselves on the back for a job well done.

Administration officials said Pence, always sceptical of Flynn's usefulness, had told others in the White House that he believed Flynn lied to him.

The retired general's departure makes him one of the shortest-serving senior security officials in US history. His withdrawal as a keynote speaker at a special operations forces banquet on Monday night was a straw in the wind after days in which Trump refused to express confidence in him.

His ignominious resignation comes amid reports that the US intelligence agencies now withhold sensitive intelligence from their presidential briefings, a follow-on from earlier inside accounts alleging that those agencies had taken to advising their foreign counterparts not to share intelligence that they could not afford to have revealed by an administration that leaks like a sieve.

In his letter of resignation to Trump, Flynn defended himself, claiming his intention was to "facilitate a smooth transition" and that he was trying "to build the necessary relationships" for the new administration.

"Unfortunately, because of the fast pace of events, I inadvertently briefed the Vice-President-elect and others with incomplete information regarding my phone calls with the Russian ambassador," Flynn wrote. "I have sincerely apologised to the President and the Vice-President, and they have accepted my apology."

Speaking on background, a senior White House official told reporters that Flynn walked – Trump did not push him. The National Security Council's chief had quit, he said, because of "the cumulative effect" of damaging news coverage about his communications with the ambassador.

Flynn's position was further eroded by a report on Monday, in The Washington Post, that in late January, then acting attorney-general Sally Yates told the White House that in misleading Pence, Flynn had left himself open to Russian blackmail – and that the outgoing national intelligence and CIA directors had agreed with her assessment.

The Trump administration can now expect to come under pressure for having stood by Flynn in subsequent weeks and, seemingly, not to have acted on the Yates warning.

On Monday, the White House sent conflicting signals on Flynn's fate.

Spokesman Sean Spicer said that Trump was "still evaluating" the revelations on Flynn's call to the ambassador and his subsequent efforts to conceal the nature of the conversation. Working from a completely different song sheet, White House counsel Kellyanne Conway insisted during an appearance on MSNBC that Flynn "does enjoy the full confidence of the President".

By some accounts, there is ambiguity in the transcript of the Flynn-Kislyak conversation. But that Flynn made the call feeds a deep distrust of him in particular, and the Trump administration in general, over their as-yet unexplained close dealings with Moscow, which include a paid appearance by Flynn at a December 2015 event in Moscow, hosted by the Kremlin-funded Russia Today cable channel – at which Flynn was honoured with a seat at Russian President Vladimir Putin's dinner table.

As Flynn resigned, The New York Times reported that he was also under investigation by the US Army over the payment for his Moscow appearance which, if proved, may be breach of the emoluments clause of the Constitution, which bars former military officers from receiving money from foreign governments without congressional approval.

"[Flynn's] unpardonable sin was hanging the Vice-President out to dry," Republican strategist Matt Mackowiak said.

Flynn's struggle to survive coincides with a raft of seemingly well-sourced reports, from inside the administration and the agencies on a presidential transition wracked by unprecedented chaos and distrust.

Flynn's National Security Council is described as anxious and chaotic – as staff struggle to make policy sense of Trump's tweets while looking over their shoulders as their loyalty is questioned over multiple leaks.

In reconfiguring the NSC, Trump has increased the military staff numbers, many of them Flynn acolytes, meaning that greater emphasis is given to military solutions than to diplomatic. At the same time, the NSC standing of the military and intelligence chiefs has been downgraded and the executive order by which Trump appointed Bannon to a permanent NSC post had to be re-issued to ensure that Trump's new CIA chief, Mike Pompeo, had the same standing.

The intelligence agencies' refusal to issue a security clearance for one of Flynn's senior deputies was read in some quarters as payback for Flynn's charges that the agencies' work on Russia, in particular, was inadequate and politically motivated – but Pompeo backed the agencies' decision.

Flynn, who was sacked by the Obama administration from his job as chief of military intelligence, has also seemed out of his depth, revealing surprise on being informed that both the State Department and Congress had key roles in deciding foreign arms sales and technology transfers. Apparently he was of the belief that Trump could unilaterally agree new weapons sales to Saudi Arabia and the United Arab Emirates.

A CNN report on Friday said intelligence sources had confirmed the veracity of much of the content of what has been described as the "dodgy" dossier – the explosive 35-page report by a former senior British intelligence agent.

Conversations between foreign nationals as described in the dossier did take place – and those involved were known to US intelligence to have been "heavily involved" in collecting information damaging to Hillary Clinton and helpful to Donald Trump.

There has been no confirmation of the salacious aspects of the dossier – in particular, that Russia had a compromising "sex tape", purportedly recorded when Trump was in Moscow in 2013.

Former NSC analyst and counter-intelligence officer John Schindler wrote: "I can confirm from my friends still serving in the [intelligence community] that [the intelligence] which corroborates some of the dossier, is damning for the administration. Our spies have had enough of these shady Russian connections - and they are starting to push back."

Schindler quotes a senior Pentagon intelligence official who told him: "'Since January 20, we've assumed that the Kremlin has ears inside the White House Situation Room – there's not much the Russians don't know at this point,' the official added in wry frustration."

Flynn had a reputation for making dubious, ill-founded statements and for having no regard for documented facts. During his term as chief of the Defence Intelligence Agency (DIA), from which he was sacked for managerial incompetence and poor judgment, his staff coined the term "Flynn facts".

In December, Trump sacked Flynn's son from his transition team for tweeting the bogus claim that Clinton and other senior Democrats were running a child sex ring through a Washington pizzeria – but he spared the father who also tweeted such nonsense.

On Monday night, the father copped it too.