Women, children and religious minorities will be prioritised in a new UK resettlement scheme for 20,000 Afghan refugees, Boris Johnson will announce, acknowledging that those who helped the western coalition over two decades are now most at risk from the Taliban takeover.

But most of the 20,000 are likely to have fled to neighbouring countries such as Pakistan before being resettled in Britain over five years, a Whitehall source said, unless the UK can strike an agreement with the Taliban to let people depart.

Johnson said the UK owed “a debt of gratitude to all those who have worked with us to make Afghanistan a better place over the last 20 years” and “many of them, particularly women, are now in urgent need of our help”.

Ahead of the recall of parliament on Wednesday, the prime minister added: “I am proud that the UK has been able to put in place this route to help them and their families live safely in the UK. The best solution for everyone is an Afghanistan that works for all Afghans.

“That means the international community coming together to set firm, political conditions for the country’s future governance. And it means focusing our efforts on increasing the resilience of the wider region to prevent a humanitarian emergency.”

Johnson spoke to the US president shortly after finalising the settlement scheme. No 10 said Joe Biden and he agreed to keep cooperating over the evacuation plan. “They resolved to continue working closely together on this in the days and weeks ahead to allow as many people as possible to leave the country,” a No 10 spokesperson said.

They said that Johnson had “stressed the importance of not losing the gains made in Afghanistan over the last 20 years” and that the pair would speak again at a virtual meeting of G7 leaders in the coming days.”

The home secretary, Priti Patel, said refugees could “start a new life in safety in the UK, away from the tyranny and oppression they now face”.

The scheme is similar in size and scope to one for Syrians under which 20,000 people have been resettled since 2014, prioritising survivors of torture, people with serious medical conditions and women with children.

However, questions are likely to be raised as to why the number is similar given Afghanistan’s population is double that of Syria and the UK has been an active participant in the conflict.

Lord Dubs, a former child refugee, said the programme was not ambitious enough. “If the Canadians can take 20,000, why are we only taking 20,000 over five years?” the Labour peer said. “I think the criteria for prioritising women and children and vulnerable people is right, but these people are in danger now and are in desperate need for safety.”

Dubs said ministers had previously been “sneering” towards Afghan men in Calais and Greek refugee camps and refused to believe they were fleeing the threat of Taliban recruitment. “Are we going to believe them now?” he said.

The scheme will allow 20,000 Afghans to settle in the UK, expected to happen over five years. Of that total, it is planned that 5,000 will arrive by the end of 2021. The programme will run separately to the Afghan relocations and assistance policy (Arap), launched in April, which offers relocation for those who aided British operations in Afghanistan.

“We don’t want to do this on the basis of whoever can get themselves to Kabul airport over the course of the next week,” one Whitehall source said. “In practice that means most people will be coming via third countries.”

Hundreds of evacuees arrived in the UK on Tuesday, including 250 on a flight due to touch down at RAF Brize Norton late in the evening, airlifted out because either because they were Britons, dual nationals or Afghans eligible to come to the UK on the Arap scheme.

There are an estimated 3,000 Britons and dual nationals still in the Taliban-controlled country plus a further 3,000 Afghans eligible for resettlement in the UK under Arap.

Those who have fled Afghanistan will be able to apply from any other third country, the Home Office confirmed, with all subject to national security checks. Whitehall sources indicated that a “small number” of people who applied under Arap failed national security tests and were barred from flying to the UK. The overall national security threat posed by extremist groups in Afghanistan to the UK is not deemed to have changed in the light of the Taliban takeover.

Patel chaired an emergency meeting with her Five Eyes counterparts to try to develop a consensus on safe routes for refugees, the Home Office said. Canada announced it will take 20,000 Afghan refugees and the US appears likely to resettle up to 30,000.

The UK scheme’s announcement followed criticism aimed at the Foreign Office over chaotic scenes in Kabul as military personnel were drafted in to deal with visas, overseen by the UK ambassador who remained in the country to sign off applications.

Diplomatic sources have been highly critical of the foreign secretary, Dominic Raab, who returned from holiday on Sunday. One source claimed Raab had not talked to key UK ambassadors in countries likely to come under significant pressure after the Taliban victory, including Pakistan, Uzbekistan and Iran. The Foreign Office did not dispute this but said he had been in constant contact with key officials.

A Foreign Office source said the blame should not be laid solely at the door of the UK, insisting the failure to predict the speed at which Afghanistan would fall was a “massive failure of the international community”.

Raab said the UK would reconsider its aid budget for Afghanistan, which could increase by 10% – though the fund has already been cut by more than three-quarters. Johnson is expected to announce further details of additional humanitarian aid and diplomatic support in the Commons on Wednesday, when parliament will be recalled to discuss the situation in Afghanistan.