Karen Wheeler’s resignation stokes fears the UK will not be ready for a no-deal Brexit by October

The government official in charge of delivering “frictionless” Brexit border arrangements, including emergency plans for Dover and Ireland in the event of no deal, has quit just two years into her job.

Karen Wheeler, director general of Her Majesty’s Revenue & Customs Brexit border delivery group, was the lead official coordinating a cross-Whitehall response involving police, ports, customs and freight interests.

Her departure is being seen as a blow to the government and increasing the risk that the UK will not be as prepared for a possible no deal on 31 October.

“Nothing is happening in Whitehall now. Lots of people have been stood down on Brexit no-deal preparations and there is a general risk that people are just going to see this hiatus as an opportunity to clear off and go into the private sector,” said a source who knows Wheeler.

Jon Thompson, HMRC’s chief executive, said in a statement: “I would like to thank Karen for her outstanding work leading the Border Delivery Group to prepare the UK for EU exit and we wish her well for her retirement. We shall be announcing her successor in due course.”

Thompson is seen as one of the most brutally honest Whitehall officials in relation to the realities of Brexit, and his openness in multiple appearances in House of Commons select committees warning of ballooning costs of border arrangements has had a knock-on effect in the culture of the department.

It meant officials were unafraid of politically inconvenient truths, including Wheeler, who earlier this year said there were no magic technological solutions for preventing a hard border with Ireland in the event of no deal.

Wheeler said the UK would need a customs union with the EU, plus something that looked like a single market, to have completely free movement of goods across the border between Northern Ireland and Ireland. She was appointed as director general for border coordination at HMRC on 3 July 2017.

HMRC declined to comment further on Wheeler’s departure, but there will be fears that other senior officials, including Theresa May’s chief Brexit negotiator, Olly Robbins, may also use the hiatus to seek pastures new.

Joe Owen, the Institute for Government’s Brexit programme director, predicted earlier this week that “many of the 16,000 civil servants working on Brexit will now be looking for a change of scenery”.

Wheeler is the second senior official to leave in as many months. Philip Rycroft, the civil servant in charge at the Department of Exiting the EU, left on 29 March, even though the UK did not, Owen noted.

“There is likely to be even more churn in the levels below, even if it’s not as visible externally,” he said. “By October, with the Brexit deadline rapidly approaching, the officials in some of the key no-deal jobs could have been in post for little more than a few months.”