Civilian evacuations from Afghanistan will finish on Saturday, the head of the UK armed forces, Gen Sir Nick Carter, has said.

With very few civilian flights remaining, Carter said it was heartbreaking that the evacuation had failed to get everybody out. “We’re reaching the end of the evacuation, which will take place during the course of today,” he said.

“We haven’t been able to bring everybody out and that has been heartbreaking. There have been some very challenging judgments that have had to be made on the ground. We are forever receiving messages from our Afghan friends that are very distressing, so we’re all living this in the most painful way.”

Speaking on BBC Radio 4’s Today programme, Carter said the final stages of the evacuation were going according to plan. “It’s gone as well as it could do in the circumstances,” he said.

On Friday the defence secretary, Ben Wallace, publicly accepted that there would be up to 1,100 Afghan nationals left behind by the evacuation effort, including Afghan translators and other who worked with UK forces.

Gen Sir Richard Barrons said it was going to be a slow process but the UK had no choice but to cooperate with the Taliban in order to get the rest of its people out of Afghanistan.

Barrons, a retired British army officer, was commander of joint forces command – now called strategic command – from April 2013 until his retirement in April 2016.

He told Times Radio: “What we need to recognise is we are where we are and it is in our own strong, national interest to find a way to get those 1,100 or so people we have a commitment to, who are still stuck in Afghanistan, out and to cooperate with the Taliban in order to stop terrorism coming to the UK.

“We are going to have to be pragmatic. I think this will be quite a slow process. It will be conditional, but it is necessary.”

Speaking about Thursday’s suicide bombing outside Kabul airport, Barrons said: “What it does do is illustrate that Isis-K [Islamic State Khorasan Province, or ISKP] is a risk to the United Kingdom, here at home, and to our interests abroad.”

A Royal Air Force plane carrying soldiers landed at the RAF Brize Norton airbase north-west of London on Saturday morning. The troops are part of a contingent of 1,000 that have been based in Kabul to help run the airlift.

The shadow defence secretary, John Healey, told Sky News he also expected the operation to wrap up within 24 hours, despite leaving behind Afghans at risk of Taliban reprisals.

Healey said: “This is the brutal truth: despite getting more than 14,000 people out, there are probably 1,000 Afghans who have worked with us over two decades in Afghanistan, helped our troops, our aid workers, our diplomats, that we promised to protect, but we’re leaving behind.

The chairman of the foreign affairs select committee, Tom Tugendhat, described the UK’s efforts to withdraw people from Afghanistan as a “sprint finish after a not exactly sprint start” and that there were “questions to be asked” of Dominic Raab, the foreign secretary.

“There’s been many of us giving pressure to improve the processing of people who we think we have a duty of care to over the months and years,” said Tugendhat. “There are going to be questions to be asked to the foreign secretary about the processing in the UK in recent weeks that we’re going to have to see what the answers are.

“We’ll certainly be looking backwards, as well as forwards, because if this were ever to happen again we need to make sure that we do not find ourselves leaving hundreds, possibly even thousands, of people behind.”

Tugendhat said people should forget about getting to Kabul and attempting to fly from the airport, because of the numerous dangerous checkpoints that have been installed along the motorways.

He said he was disappointed to see the British evacuation effort coming to an end. “I’m extremely sad about this and I very much hope that it might go beyond the August deadline … It still leaves me extremely sad that so many of my friends have been left behind.”