Boris Johnson’s government has been accused of “keeping the public in the dark” over the true cost of Brexit, as new figures show that Whitehall departments have spent at least £4.4bn on preparations for withdrawal from the EU.

And there were warnings that the figure will only increase as the prospect looms of new border checks and controls at the end of the transition period in December.

The National Audit Office study found that more than 22,000 civil servants across 18 government departments were working on Brexit preparations by the end of last year, with the task consuming 12 per cent of all senior mandarins and 5 per cent of the total workforce. If the staff working on Brexit had been gathered in one department, it would have been the sixth largest in Whitehall.

The massive bureaucratic burden of Brexit reversed an austerity drive to reduce staffing numbers on Whitehall, with the total number of senior civil servants now 9 per cent higher than in 2010.

Around £1.9bn was spent on staffing, £288m on external consultants and lawyers and £1.5bn on new infrastructure, computer systems and advertising. Some £92m was classed as “losses”, including £50m paid to ferry companies and £33m to Eurotunnel as part of the abortive efforts to provide extra cross-Channel capacity in the case of hold-ups in Dover in a no-deal situation.

Brexit day: UK says goodbye to EU Show all 66 1 /66 Brexit day: UK says goodbye to EU Brexit day: UK says goodbye to EU A message projected onto the White Cliffs of Dover Sky News/AFP via Getty Brexit day: UK says goodbye to EU LONDON, ENGLAND - JANUARY 31: Pro Brexit supporters attend the Brexit Day Celebration Party hosted by Leave Means Leave at Parliament Square on January 31, 2020 in London, England. At 11.00pm on Friday 31st January the UK and Northern Ireland exits the European Union, 188 weeks after the referendum on June 23rd, 2016. 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(Photo by Glyn KIRK / AFP) (Photo by GLYN KIRK/AFP via Getty Images) GLYN KIRK AFP via Getty Brexit day: UK says goodbye to EU A man wears a pro-Brexit t-shirt Reuters Brexit day: UK says goodbye to EU Anti-Brexit demonstrators visit Europe House to give flowers to the staff on Brexit day Reuters Brexit day: UK says goodbye to EU Pro Brexit supporter wears a novelty Union Jack top hat outside the Houses of Parliament Getty Images Brexit day: UK says goodbye to EU Customers Scott Jones and Laura Jones at the Sawmill Bar in South Elmsall, Yorkshire, where a Brexit party is being held throughout the day PA Brexit day: UK says goodbye to EU A pro-Brexit demonstrator clenches his fist during a rally in London, Friday, Jan. 31, 2020. Britain officially leaves the European Union on Friday after a debilitating political period that has bitterly divided the nation since the 2016 Brexit referendum. (AP Photo/Alberto Pezzali) Alberto Pezzali AP Brexit day: UK says goodbye to EU LONDON, ENGLAND - JANUARY 31: Pro-EU activists protest at Parliament Square as people prepare for Brexit on January 31, 2020 in London, United Kingdom. At 11.00pm on Friday 31st January the UK and Northern Ireland will exit the European Union 188 weeks after the referendum on June 23rd 2016. (Photo by Jeff J Mitchell/Getty Images) Jeff J Mitchell Getty Brexit day: UK says goodbye to EU LONDON, ENGLAND - JANUARY 31: Pro Brexit supporters hold up placards at Parliament Square as people prepare for Brexit on January 31, 2020 in London, United Kingdom. At 11.00pm on Friday 31st January the UK and Northern Ireland will exit the European Union 188 weeks after the referendum on June 23rd 2016. (Photo by Jeff J Mitchell/Getty Images) Jeff J Mitchell Getty Images Brexit day: UK says goodbye to EU Pro-EU activists protest Getty Images Brexit day: UK says goodbye to EU A pro-Brexit demonstrator burns a European Union flag AP Brexit day: UK says goodbye to EU Pro Brexit supporters Getty Images Brexit day: UK says goodbye to EU Pro Brexit supporters Getty Images Brexit day: UK says goodbye to EU A Brexit supports holds a sign in Parliament Square AP Brexit day: UK says goodbye to EU A man carries an EU themed wreath Reuters Brexit day: UK says goodbye to EU Ann Widdecombe reacts with other members of the Brexit party as they leave en masse from the European Parliament PA Brexit day: UK says goodbye to EU Anti-Brexit demonstrators in Parliament Square PA Brexit day: UK says goodbye to EU Pro EU supporters let off flares from Westminster Bridge Getty Brexit day: UK says goodbye to EU British MEPs Jonathan Bullock, holding the Union Jack flag and Jake Pugh leave the European Parliament, in Brussels on the Brexit day AFP via Getty Brexit day: UK says goodbye to EU Newspapers and other souvenirs at a store, near Parliament Square Reuters Brexit day: UK says goodbye to EU Brexit supporters hold signs in Parliament Square AP Brexit day: UK says goodbye to EU Pro-EU protesters hold placards in Parliament Square AFP via Getty Brexit day: UK says goodbye to EU French newspapers PA Brexit day: UK says goodbye to EU Sinn Fein leader Mary Lou McDonald with a Border Communities Against Brexit poster before its unveiling in Carrickcarnon on the Irish border PA Brexit day: UK says goodbye to EU National growers organisation British Apples & Pears has renamed a British apple to EOS, the Greek goddess of dawn, to commemorate Brexit day AP Brexit day: UK says goodbye to EU Pro-EU protesters hold placards in Parliament Square AFP via Getty Brexit day: UK says goodbye to EU Britain's departure from the European Union was set in law on January 29, amid emotional scenes, as the bloc's parliament voted to ratify the divorce papers. After half a century of membership and three years of tense withdrawal talks, the UK will leave the EU at midnight Brussels time (23.00 GMT) on January 31 Reuters Brexit day: UK says goodbye to EU A man poses with paintings on Parliament Square Reuters Brexit day: UK says goodbye to EU People sporting Union Flags gather in Parliament Square Getty Brexit day: UK says goodbye to EU A man walks with a St. George's flag at Westminster bridge on Brexit day Reuters Brexit day: UK says goodbye to EU A British bulldog toy and other souvenirs at a souvenir store Reuters Brexit day: UK says goodbye to EU British pro-brexit Members of the European Parliament leave the EU Parliament for the last time Reuters Brexit day: UK says goodbye to EU Jonathan Bullock waves the Union Jack as he leaves the European Parliament EPA

Brexit preparations soaked up £1 out of every £100 of planned government spending, at a time when many departments were experiencing real-terms cuts.

But the NAO figure does not include spending after 1 January this year, losses caused by diverting staff and resources away from departmental responsibilities or future costs such as the £30bn divorce settlement and the ongoing bill for additional red tape. And it does not cover additional costs to businesses and individuals from EU withdrawal.

The report said that departments had made “little” information public on how they spent the funds set aside for Brexit preparations, and NAO boss Gareth Davies said it exposed “limitations” in the way ministers monitored the spending.

The chair of the European Movement, former Conservative cabinet minister Stephen Dorrell, said the report highlighted “the astounding cost of Brexit that has been hidden from the public”.

“The lack of detail and limited data contained in the report is indicative of the secretive way that the government is delivering Brexit,” said Mr Dorrell.

“Boris Johnson is insisting on delivering one of the greatest constitutional changes in half a century behind smoke and mirrors, without the democratic accountability we expect of our government.”

The chair of the influential House of Commons Public Accounts Committee, Meg Hillier, said: “The public has been kept in the dark as to what the government has been doing. Data is limited, and the Treasury seem unconcerned by the lack of transparency.”

And Liberal Democrat Brexit spokesman Alistair Carmichael called on ministers to “come clean” on exactly how the Brexit billions were spent.

"Billions of pounds have been thrown away in a bid to paper over the Tories' Brexit mess,” said Mr Carmichael. “The public have a right to know where it is all going. In the face of major floods and the coronavirus threat, we have to ask if the government knows its own spending priorities.”

Chancellors Philip Hammond and Sajid Javid made a total of £6.3bn available to government departments and devolved administrations between June 2016 and March 2020 to prepare for EU exit, including £2bn for the eventuality of no-deal.

With no-deal Brexit still a strong possibility, and prime minister Boris Johnson indicating that he may decide as early as June to quit on World Trade Organisation terms, it is unclear how much of this money will eventually be spent.

The government staged trials of traffic management systems to prepare for a no-deal Brexit (Rex)

Naomi Smith, the chief executive of the Best for Britain campaign, said: "An awful lot of money has been spent by government departments on the process of leaving the EU.

"And those costs will only soar as we approach June without the government budging at all on its negotiating stance.

"We've spent billions on this when to be frank there are other priorities we should be focusing on. With coronavirus looking like it will wreak havoc for months to come, let's support our NHS at this critical time instead."

Biggest Whitehall spenders on Brexit preparations were the Department for Environment, Food and Rural Affairs, which spent £871m; the Home Office (£803m); and HM Revenue & Customs (£748m). The Cabinet Office reported a communications spend of £49m, including funding for the "Get ready for Brexit" campaign in the run-up to the 31 October deadline for withdrawal, which was missed.

Major infrastructure spending included the Operation Brock system to manage traffic disruption in Kent, which was forecast to reach £69m by the end of 2019-20.