Civil servants working for the Department for Exiting the European Union have been awarded nearly £1.3m in bonuses, new figures show.

DExEU disclosed on Thursday that it had paid out £350,000 in bonuses in the year after the referendum. This is in addition to the revelation last month that it had paid out £1m in performance-related awards for April 2017 to March 2018.

It made the late disclosure on its first-year bonuses on Thursday in a bid for full transparency, it said.

The department paid £343,650 to delegated graded civil servants, in amounts ranging from £700 to £2,500, for the year 2016 to 2017.

In its annual report for 2018-19 also published on Thursday, it revealed that the highest-paid official was the recently retired permanent secretary, Philip Rycroft, who earned between £225,000 and £230,000 including benefits in kind of £17,900 and a pension of £46,000. His benefits in kind included travel costs between home and work.

About 16,000 civil servants have been working on Brexit at an estimated cost of £1.5bn to date. While no-deal planning has continued across Whitehall, some staff working on emergency Operation Yellowhammer duties were stood down in April by the Cabinet Office when article 50 was extended until Halloween, after an estimated £1.5bn had been spent including on recruits from the private sector.

Now departments are expected to be ordered to ramp up no-deal planning immediately after the new prime minister, expected to be Boris Johnson, gets into No 10 next Wednesday.

It is not known who is going to be on his Brexit team but the attorney general, Geoffrey Cox, is being tipped, as is the pro-Brexit trade consultant Shanker Singham as an adviser.

He is the leading force at the privately funded Alternative Arrangements Commission, which has sought to find solutions to the Irish border question. It is understood he has not been approached but would be willing to work on a Johnson or Hunt team.

It is thought all big Whitehall departments have made Brexit bonuses but virtually all have refused Guardian freedom of information requests for disclosure.

So far the House of Commons is the only other department to disclose its payments.

Last month, it revealed it had made £700,000 in extra payments involving a £250 bonus to all 2,800 Commons administration and parliamentary Digital Service staff in recognition of their hard work sitting additional days and working into the night.

The departments that did respond to freedom of information requests include the Ministry of Defence, which said it paid 19 staff “a reward” or gave them a “thank you” voucher for their work on Brexit up to April 2019.

In March, the armed forces mobilised a special team in a 24-hour cover in a nuclear-proof bunker under their headquarters as part of the military’s crisis management operation, dubbed Operation Redfold.

They were due to direct 3,500 military personnel on standby if required in the case of chaos on the streets, which could have included congestion on the roads to Dover, disruption to medical supplies and aviation.

The MoD said it had paid out a total of £8,250: the highest award was £2,000 and the smallest £100.

The Food Standards Agency paid out almost £30,000 to 64 staff in bonuses ranging from £250 per person to £1,000, while the Medicines and Healthcare products Regulatory Agency paid seven staff between £500 and £800 in a Brexit bonus.

It is responsible for the safety of medicines and medical devices, many of which come from the EU.

While virtually all the big departments refused to disclose Brexit bonus data, some did reveal what they had spent on Brexit so far.

DExEU spent £101.6m in the year 2017-18.

Her Majesty’s Revenue and Customs spent £308m on Brexit: £47m in 2017-18 and £261m for the financial year 2018-19.

The Home Office, which was responsible for developing the settled status scheme for EU citizens, spent £70m in the year 2017-18.

The Ministry of Justice revealed it had spent £9.7m on Brexit-related work in 2018-19.

The Cabinet Office, the Environment Agency, and the Department for Infrastructure in Northern Ireland said they did not award bonuses.

The National Police Chiefs’ Council revealed that the International Crime Coordination Centre, which was set up to provide continuity for UK law enforcement following Brexit, said it spent £18,000 in 2017-18 and £1.75m in the year 2018-19.