The extraordinary spectacle of one of Britain’s most senior civil servants being forced to retract evidence he had given to MPs just hours earlier is an illustration of the simmering discord within Whitehall over the handling of the coronavirus crisis.

The letter from Sir Simon McDonald to the Foreign Affairs Committee completely backtracked on what he had stated was one of the main reasons behind the government not joining a EU programme on medical equipment, and led to the immediate charge that he had been subjected to political pressure.

Sir Simon, permanent under-secretary at the Foreign Office, had told the MPs, about the programme: “All I can say is that it is a matter of fact that we have not taken part. It was a political decision . And the decision was no.”

Five hours later this had changed to: “Due to a misunderstanding, I inadvertently and wrongly told the committee that ministers were briefed on the joint EU procurement scheme and took a political decision not to take part in it. That is incorrect. Ministers were not briefed by our mission in Brussels about the scheme and a political decision was not taken on whether or not to participate.”

The letter had come after frantic calls in the Foreign Office, the Department of Health, and Downing Street: Dominic Raab, Matt Hancock, and Boris Johnson’s advisors, with the foreign secretary and acting prime minister said to have been angry that he had not been made aware of what Sir Simon was going to say to the committee.

The retraction was an incredible volte-face. At a very basic level, the clear inference, if one took the retraction at face value, was that Sir Simon, the head of the diplomatic service, and a former foreign policy advisor at No 10, a highly respected official who had served in the US, Germany and Saudi Arabia, had got a crucial fact on an important issue totally wrong.

“There seems to be a sort of Ministry of Truth now, and only they have the right to give out information, this has been a pattern for a while now with [government] departments across the affected”, said a civil servant.

“But what happened with Simon McDonald was simply wrong on many levels.”

Sir Simon seemed to be unaware of this Orwellian diktat or of the controversy about to erupt over his evidence. His first tweet after appearing at the session was a sunny “just gave evidence to @CommonsForeign 1st time via video link. Breaking new ground remote-working during Covid 19 #Lockdown. But Parliament still requires participants to be smartly dressed.”

Downing Street’s position is that the UK was making its own arrangements on the equipment because it was no longer part of the EU: Brexit sentiments had played no part in the decision. It later admitted that the UK had been invited to take part in the programme, but officials missed the email because of a “communications confusion”.

Chris Bryant, a Labour member of the committee who was among those who questioned Sir Simon, was clear in his opinion of what happened.

“It’s all nonsense, he had been leant on. The whole thing stinks of people trying to cover their tracks… It seems that not content with refusing to take part in a mass EU purchase of desperately needed vital equipment out of a fit of Eurosceptic pique, the government has repeatedly told fibs in a sad attempt to cover its tracks,” he told Sky News.

It is not just the Foreign Office which is finding itself under tremendous pressure not to stray in any way from the government hymn sheet on Covid-19.

Officials in other government departments say they are in the same position. Officials from the Ministry of Defence and the British military dealing with the pandemic find themselves in the firing line if they are deemed to be “off message” over the crisis. They have also found that Downing Street wants to be in control of disseminating information at almost every level.

Sir Simon is the most senior Whitehall figure who has fallen out of line so far and there is disquiet among many of his colleagues about what has unfolded. A former British ambassador who later worked for another government service said: “Let’s accept that maybe there really was a misunderstanding. Maybe this was a ministerial decision on the EU scheme rather than a purely political one, that can be possible. But what the letter says, what he had to write, does put Simon in a difficult position.”

The crux of the matter is whether ministers were told by officials about the EU programme. The BBC says that sources present at Cobra meetings have revealed that there were discussions on whether to work with the EU at the start of the pandemic.

One minister present, according to the BBC, said no decisions were made during the meetings, but it was clear that there was an “added dilemma” because of the politics of Brexit. Sources close to Matt Hancock, the health secretary, strongly dispute there was any discussion about specific EU schemes.

A senior Whitehall official maintained to The Independent that information about the EU programme was passed on to ministers.

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“I am told that there was material provided about the Joint Procurement Agreement, this was in some detail because we are talking about four separate procurement schemes for different things in the programme,” he said. “I do not know if it was discussed in Cobra, I would be very surprised if it wasn’t.”

Asked who had lent on Sir Simon to change his evidence, a Downing Street spokesperson insisted: “Nobody, it is important that select committees are given accurate information and that’s why he corrected what he had said. He took the opportunity to correct the record very quickly and in a very clear way.”

Asked whether the prime minister still had confidence in Sir Simon, the spokesperson responded: “Yes,” holding that the only EU-related discussions in Cobra at the time in question related to the repatriation of nationals from China.

While recriminations mounted in London, in Brussels the European Commission wanted to stress that the UK chose not to join the programme.

A spokesperson said: “Supplies of the member states was a recurring topic of the agenda of the health and security committee meetings. The UK was, as all other members of the health security committee meetings, aware of the work that was ongoing and had ample opportunity to express its wish to participate in a joint procurement if it wanted to do so. As to why it did not participate, this is obviously something on which we cannot comment.”

UK's failure to join EU ventilator scheme was 'political decision', not communication error, says senior civil servant

One of Sir Simon’s previous appearances before the Foreign Affairs Committee was in July last year when he answered questions about Sir Kim Darroch, the British ambassador to Washington who resigned after his diplomatic emails critical of Donald Trump were leaked.

One key factor behind Sir Kim’s resignation was that Boris Johnson, then running for the Tory party leadership – and to take over from Theresa May as prime minister – failed repeatedly to give his backing to the ambassador, facing a barrage of insults from Mr Trump in a TV interview.

Sir Simon told the Committee that he had recently spoken to Sir Kim: “He had a difficult night, considering what to do. He thought about the pressure on his family. He considered that for as long as he was in Washington, he would remain a target.”