Boris Johnson accepted decisions could have been made quicker during the evacuation of Afghanistan but praised the “outstanding” efforts of those involved following damning testimony from a Foreign Office whistleblower.

Former official Raphael Marshall, who worked for the Foreign Office during the effort, claimed that just 5% of Afghan nationals who applied to flee under one UK scheme received help as a result of the “dysfunctional” and “chaotic” handling of the situation.

The Prime Minister and his deputy Dominic Raab both defended the Government’s actions during the summer, when Afghanistan was overrun by the Taliban leaving thousands seeking to escape from Kabul airport.

Mr Marshall told MPs that some of those hoping to escape were murdered after being left behind in Kabul.

The Prime Minister told reporters “sometimes decisions took hours longer than we wanted” during the evacuation from Kabul, but “you have to be careful about how you do it, it was still an astonishing thing to get 15,000 people airlifted out of Kabul in pretty harrowing circumstances”.

The Operation Pitting airlift was “one of the outstanding military achievements of the last 50 years or more”, he added.

Mr Johnson also dismissed as “complete nonsense” a claim that he intervened to request help to evacuate animals from a shelter run by former Royal Marine Paul “Pen” Farthing.

Mr Marshall had claimed that the Prime Minister requested that “considerable capacity” was made available to transport the Nowzad shelter’s animals, putting the lives of troops at risk to help aid their departure on a privately-funded plane.

In written evidence to the Commons Foreign Affairs Committee, Mr Marshall alleged that then foreign secretary Mr Raab “did not fully understand the situation”, was slow to rule on cases and requested they were reformatted “in a well-presented table” before making a decision.

Mr Raab, who was moved to become Justice Secretary and Deputy Prime Minister after his handling of the crisis, sought to defend his record, having already been heavily criticised for holidaying in Crete as the Taliban were storming back to power in Afghanistan.

“It’s inaccurate in certain respects, the suggestion that junior desk officers were making decisions is just not correct,” he told BBC Radio 4’s Today programme.

“There’s a difference between processing and deciding, so I’m afraid I don’t accept that characterisation.

“On the charge it took several hours to make decisions, we’re not talking about days, it’s not been suggested weeks, but several hours to make sure we had the facts, and that, as between myself, the Home Secretary and the Defence Secretary, decisions were made and actually I would suggest that’s a reasonably swift turnaround.”

One of Mr Marshall’s allegations was that at one point the Cabinet minister “declined to make a decision” on whether to admit a group of women’s rights activists “without a properly formatted submission with a table setting out multiple cases”.

It would have been reasonable for Mr Raab to defer to the crisis centre’s judgment but “in the circumstances it is hard to explain why he reserved the decision for himself but failed to make it immediately”, the former official said.

Mr Raab responded: “I make no apology for saying I needed the clear facts that each case presented precisely so we can make swift decisions.

“Some of the criticism seems rather dislocated from the facts on the ground, the operational pressures that with the takeover of the Taliban, unexpected around the world… I do think that not enough recognition has been given to quite how difficult it was.”

Among the flaws alleged by Mr Marshall was that the process of selecting who could be airlifted out was “arbitrary and dysfunctional” and that thousands of emails were going unread.

He said that Foreign Office colleagues were “visibly appalled by our chaotic system” which was put in place as foreign forces withdrew after a 20-year occupation of Afghanistan.

Taliban resurgence in Afghanistan
Lt Cdr Alex Pelham Burns, a member of the UK Armed Forces during the evacuation of entitled personnel from Kabul airport (Ministry of Defence/PA)

Mr Marshall, who worked in the Afghan Special Cases team handling the cases of Afghans who were at risk because of their links with the UK, estimated “between 75,000 and 150,000 people” including dependents applied for evacuation under the “leave outside the rules” category.

But he calculated that “fewer than 5% of these people have received any assistance” and stated that “it is clear that some of those left behind have since been murdered by the Taliban”.

Asked if he recognised the whistleblower’s figures, Mr Raab told Sky News: “I don’t. But what is certainly true is that we had a lot of people rushing to get out of Afghanistan for all sorts of reasons.”

Mr Marshall said “desperate and urgent” emails, including those with titles such as “Please save my children”, were also being opened but not actioned, he said.

“I believe the purpose of this system was to allow the Prime Minister and the then foreign secretary to inform MPs that there were no unread emails,” Mr Marshall wrote.

He also claimed that at one point he was the only person monitoring an inbox where pleas for help were directed.

Labour leader Sir Keir Starmer said Mr Raab should have resigned over the Afghanistan crisis.

“It is shocking that we are all now learning that emails and letters that we sent in to the Foreign Office – including from my office – were opened but haven’t been actioned.

“It’s a total failure of political leadership with an ex-foreign secretary who was busy on the beach instead of doing his job.”