The chief executive of the civil service has said the government will never be fully prepared for Brexit as he revealed plans to move up to 5,000 staff into an emergency command and control centre in the event of no deal. 

John Manzoni said the civil service had already hired 10,000 people to cope with Brexit with another 5,000 in the pipeline. 

But he warned: “The longer it goes on, the better we are prepared, but we still won’t be completely prepared.” 

He was speaking at the launch of Whitehall Monitor 2019, an Institute for Government report, which laid bare the cost of Brexit on governing the country, with a fifth of major non-Brexit projects at risk as exiting the EU chokes the system. 

Implementing Brexit has been described as “the biggest, most challenging peacetime task the civil service has faced”, yet officials will have less time than London had to deliver the Olympics, the report finds. 

“If the UK leaves without a deal, deadlines for implementing new arrangements would be tighter still,” it says. “ The government could only expect to have ‘a fraction’ of the necessary processes and systems in place – such as ensuring that the UK complies with international law – by exit.” 

Only five of the 13 bills the government has said it needs to pass before Britain leaves the EU have made it through parliament, it finds. 

Manzoni confirmed reports of government departments commandeering volunteers for a new “command and control” emergency operation, which would be put in place in the event of no deal. 

“If we find ourselves in a sort of crash-out no deal, we have to put some operational capability into place, which is a few thousand – that is largely because people will be working 24/7 in a command and control mode; that’s the next focus; we are largely ready with that and part of the preparations as we get closer is that last act of getting those people to move,” he said. 

He said he did not have the precise number to hand of those involved but put it at “a bit less than 5,000” . 

Time for Brexit transition compared with other projects.  Photograph: Institute for Government

The report claimed that Brexit was endangering the progress of at least 26 projects designed to improve life in the UK, including the HS2 high-speed rail line. 

“I’ve never pretended it’s all going to go swimmingly well in the event of a no deal,” said Manzoni, who said the civil service was in constant engagement with the government over national priorities apart from Brexit. 

The report says staff numbers in the civil service have risen to levels not seen since the second world war, yet a hung parliament coupled with Brexit “have constrained the government’s ability to pass legislation”. 

High turnover of civil service staff is proving both expensive – costing up to £74m each year – and disruptive, as knowledge and expertise is lost. 

In the last year, some departments, including the Treasury, lost two in five of their civil servants, either to other departments or to roles outside the civil service, partly due to Brexit.  One-third of Treasury staff are working on Brexit. 

The unprecedented number of ministerial resignations – 21 since the 2017 general election, has also caused disruption, as it means only half of current cabinet ministers and half of all ministers took on their role only in 2018. 

This has taken a toll on progressing government priorities with a fifth of 133 major non-Brexit projects now endangered. 

A Cabinet Office spokesperson said Brexit negotiations were “a priority for the government” but it continued to “tackle the other issues that matter to people including backing the long term plan for the NHS” and housing plans.