The Home Office rejected an appeal from the foreign secretary, Yvette Cooper, that would have protected outstanding students in some of the world’s most dangerous countries from changes to the UK’s immigration system, the Guardian understands.

Shabana Mahmood, the home secretary, turned down proposals from the Foreign Office to maintain a carve-out for Chevening scholars, a government-funded programme for “exceptional individuals” to study for a master’s degree at a UK university.

Cooper is understood to be particularly concerned about the impact of the decision on vulnerable women in some of the most volatile parts of the world including Afghanistan and Sudan.

Her concerns are reflected across the wider Labour party, where there is firm support for the Chevening route, which brings more than 1,000 graduates to British universities from across the globe every year, fostering cultural, business and diplomatic links that persist after the students return home.

The home secretary suspended student visas for applicants from Afghanistan, Cameroon, Myanmar and Sudan last week, saying she was “taking the unprecedented decision to refuse visas for those nationals seeking to exploit our generosity”.

All outstanding Chevening applications from the four countries were cancelled and candidates informed that their applications had been terminated, despite the commitment students make to return to their home country for at least two years after the scholarship ends.

A Home Office spokesperson said: “Study routes are being widely abused, creating a back door to claim asylum into this country. That is why we are taking unprecedented action to suspend routes from four countries.

“We cannot allow exceptions to study routes to prevent further abuse across our migration system.”

The Home Office said that asylum applications from those countries grew by over 470% between 2021 and 2025 – making them among the most likely nationalities to claim.

However, critics said the government’s claims of visa exploitation are a distortion, given that – for example – just 120 Sudanese students applied for asylum in the year up to September.

Sudan, Cameroon and Myanmar are all in the midst of armed conflicts, while Afghanistan has faced a worsening humanitarian crisis since the Taliban takeover in August 2021, following the withdrawal of western troops.

Labour peer Jan Royall, a former principal of an Oxford college, told the Lords last week she was “deeply concerned” about the plans to halt student visas, quoting a former academic colleague who said “it feels like the government is joining the Taliban” by blocking the education of Afghan women.

Many Labour MPs are worried more generally about the home secretary pressing on with hardline immigration policies including an end to permanent refugee status and the removal of state support from some asylum seekers.

Mahmood’s plans, intended to be Labour’s response to the competition it faces from Reform UK, came after the party’s byelection loss to the Greens in Gorton and Denton, which has left MPs feeling anxious about losing more support on their progressive flank.