Sir Ivan Rogers says negotiating experience is in ‘short supply’ and that politicians disliked his warnings of pitfalls in his resignation email.

Britain’s ambassador to the European Union Sir Ivan Rogers dealt a blow to the UK’s Brexit negotiations by quitting and urging his fellow British civil servants in Brussels to assert their independence by challenging “ill-founded arguments and muddled thinking”.

Sir Ivan Rogers said, in an email explaining his reasons for his abrupt departure to the UK’s Brussels diplomatic staff at UKRep, that he was leaving now to give time for his successor to take charge of the lengthy negotiations process which starts in March. But he also made it clear that he had been frustrated by politicians who disliked his warnings about the potential pitfalls in the Brexit process.

He also revealed that the basic structure of the UK Brexit negotiating team had not yet been resolved, let alone a negotiating strategy.

Rogers has been attacked by Tory sceptics for warning that it may take as long as 10 years for the UK to fully break from the EU. Downing Street insisted at the time that the ambassador had been communicating the views of some European leaders, rather than giving his own assessment. He has also been repeatedly criticised for setting out how other EU leaders view the Brexit process.

He wrote to staff: “I hope that you will continue to be interested in the views of others, even where you disagree with them, and in understanding why others act and think in the way that they do.”

Rogers also defended the importance of the UK’s civil service knowledge in Brussels in his resignation email, saying: “In any negotiation which addresses the new relationship, the technical expertise, the detailed knowledge of positions on the other side of the table – and the reasons for them, and the divisions amongst them – and the negotiating experience and savvy that the people in this building bring, make it essential for all parts of UKRep to be centrally involved in the negotiations if the UK is to achieve the best possible outcomes.”

Implying that civil servants or politicians in London were trying to take over the Brexit talks, and the structure of the UK negotiating team needs “rapid resolution”, he said “multilateral negotiating experience is in short supply in Whitehall, and that is not the case in the [European] Commission or in the Council”.

He said “senior ministers, who will decide on our positions, issue by issue, also need from you detailed, unvarnished – even where this is uncomfortable – and nuanced understanding of the views, interests and incentives of the other 27”.

Rogers’ departure so close to the start of Brexit negotiations amounted to a “wilful and total destruction of EU expertise”, according to the former top civil servant at the Treasury.

In an unusually candid intervention, Lord MacPherson, who was permanent secretary from 2005 until last year, said Rogers’ decision was a huge loss and that he was the latest in a string of EU experts to be frozen out, describing the decision as “amateurish”.

MacPherson also cited Rogers’ predecessor Jon Cunliffe and Tom Scholar, previously the prime minister’s adviser on European issues who is now permanent secretary at the Treasury. His warning appears to reflect a Treasury concern that Theresa May is under pressure from Tory Eurosceptics to abandon hopes of trying to negotiate access to the profitable EU single market, even on a temporary basis.

There have been disputes across Whitehall about whether the UK can afford a so-called hard Brexit.

The Foreign Office played down the implications of the resignation, saying Rogers had been due to leave in November and that he had merely “resigned a few months early”.

“Sir Ivan has taken this decision now to enable a successor to be appointed before the UK invokes article 50 by the end of March,” a spokeswoman said.

But Rogers has known since October that he was due to leave his Brussels post before the talks are due to end in 2019, raising questions about why he was given a vital role in preparing for the negotiations in the first place.

A Whitehall source said the early departure had been discussed before Rogers told his staff on Tuesday. However, Nick Clegg, who worked with Rogers in Brussels, said it appeared to be the latest in a series of attacks on public officials who had expressed caution about Brexit.

“First it was the judges, condemned as enemies of the people for just doing their jobs,” the former deputy prime minister told the Guardian. “It’s been the CBI and any business that didn’t sign up to the Brexit zeal, and now it’s senior officials being kneecapped in the Brexit press, after Sir Ivan Rogers just gave candid advice about the length of time negotiations might take. They are in the firing line if they do not endorse a zealous world view. This is a very worrying trend, and very new in British politics.”

Insisting civil service neutrality is a precious British asset, Clegg said the government should value candid advice. “It will come back to haunt the Brexit headbangers, because you can insist as much and hysterically as you like that the world is flat, but there are only so many people you can condemn for just pointing out the truth, that the world is round and that Brexit is complicated, might take time and might not be fully to Britain’s advantage,” he said.

George Osborne, the former chancellor, tweeted praising Rogers for his work with him during meetings of EU finance ministers, saying: “He is a perceptive, pragmatic and patriotic public servant.”

Responding to Rogers’ resignation email, Lib Dem leader Tim Farron said: “It is damning when our own top people are slamming this Conservative Brexit government for using ill-founded arguments and muddled thinking.

“This is the biggest decision by the UK government in modern times and Theresa May is marching ahead without a plan or even a clue.
“We need our top people around the table if we are going to avoid wrecking the country with Brexit. It is shameful that vital, talented people like Ivan Rogers are instead being driven away.”

The Lib Dems added that it was astonishing that Rogers’ email revealed that, at this late stage in the build-up to the talks, Rogers thought that the UK had no agreed negotiating structure and, in his view, still lacked the required multilateral negotiating expertise available to the European commission.

Rogers’ remarks may reflect unresolved tensions between the UK’s Brussels diplomats and the government’s Brexit department, led by David Davis.

With the choice of Rogers’ successor bound to be seen as a signal of the direction of UK Brexit policy, Eurosceptics demanded that an enthusiastic Brexiter replace him and called for an ideological purge of officials in the Foreign Office.

Nigel Farage, the former Ukip leader, said: “No organisation has done more to give away our democratic rights than the Foreign Office. They’ve been doing it for decades and I very much hope that Sir Ivan is the first of many to go.”

John Redwood, a longtime Eurosceptic Tory MP, said: “Sir Ivan’s heart was not in the negotiations. The talks do not need to be that complicated. If you leave, you leave. You take control of your borders, your laws and your money and that is not something that needs to be negotiated with Mrs Merkel.”

Some Conservatives blamed him for under-pitching what could be achieved and for advising against taking a harder line. One adviser said: “It was not about him being a Europhile but about being difficult. He not only said the UK did not understand the EU, but [that] the EU did not understand the UK. He was just the most out front of the civil servants – but many others thought like him.”

Sources said the two main points of tension were over whether it was feasible for the UK to threaten to drop out of the EU without a deal, falling back on World Trade Organisation terms and how to persuade the EU to negotiate simultaneously on the UK’s divorce terms and a future UK-EU relationship. May has to set out her negotiation strategy to MPs in March but has so far given next to nothing away.

Dominic Raab, a Conservative MP and a member of the select committee on exiting the European Union (EEU), said it would have been more disruptive if Rogers had left in November. “Sir Ivan is a distinguished diplomat with a long record of public service,” he said. “He didn’t exactly hide the fact that his heart wasn’t in Brexit and he was due to step down in the autumn anyway. It makes sense all round to give the ambassador who will see the negotiations through some lead time.”

However, Labour’s Hilary Benn, who chairs the EEU committee, told the BBC the resignation was “not a good thing” and the government would be under pressure to get a replacement up to speed to meet Theresa May’s timetable for triggering article 50. “I think that it means that the government will have to get its skates on to make sure there is a replacement in place so he or she can work with Sir Ivan in the transition, the handover,” said the former shadow foreign secretary.

Peter Mandelson, the former Labour cabinet minister and EU commissioner, said Rogers’ experience was “second to none in Whitehall” and a serious loss for the UK negotiating team. “I would not expect him to comment further but everyone knows that civil servants are being increasingly inhibited in offering objective opinions and advice.”