Thousands of vulnerable refugees living in the UK are at risk of losing access to vital services including housing, healthcare and school places after it emerged millions of pounds of funding will come to a halt in the event of a no-deal Brexit.

The asylum, migration and integration fund (AMIF), which the EU set up in 2014, is a pot of billions of pounds to be used by EU member states to support integration of non-EU nationals, including newly recognised refugees.

Charities and non-governmental organisations (NGOs) in the UK who have received funding from the AMIF via central government have been told remaining allocations will cease immediately if the UK leaves the EU without a deal. The government has guaranteed funding for organisations that successfully bid directly to the European commission for AMIF money.

The Refugee Council, which was awarded £2.6m of AMIF funds via the Home Office to support 3,500 refugees, said the withdrawal of funding was a “disgraceful U-turn” after the British government assured it and other charities when it first awarded the grants that funding would be secure after Brexit.

The charities, which include Refugee Action, the Scottish Refugee Council, Barnet Refugee Service, RETAS and Refugee Women’s Association, estimate that the joint value of the AMIF funds are in the tens of millions of pounds and support an estimated 30,000 refugees in the UK.

Maurice Wren, the chief executive of the Refugee Council, which estimates the loss of the remaining funds will leave 1,900 refugees deprived of this vital support, said: “The support we provide to refugees through this funding is for those who are in the gravest danger – those who are very likely to end up on the streets without our support, are destitute and extremely isolated.

“The idea that such a vital service is going to be cut simply beggars belief. The government seems to have lost sight of that fact that they are dealing with the lives of real people. Such a disgraceful U-turn flies in the face of the government’s commitment to supporting refugee integration, as set out in its integration strategy.

“To date, AMIF funding has enabled the government to fulfil these promises and we have been immensely proud to see the difference it’s made to so many people’s lives. Pulling the rug from underneath this investment makes no sense. We urge ministers to overturn this decision immediately so that we can continue to help refugees build their lives and start to contribute to UK society.”

The UK government has commited to underwrite the majority of AMIF and other EU funds in the event of the UK leaving the EU without a deal, with the exception of those funds allocated by the UK responsible authority (UKRA).

A letter from the UKRA last month told organisations: “In the event that the UK leaves the EU without a deal, the UK will leave the EU budget on the day of exit meaning UK organisations, like yours, would no longer receive future funding for projects under EU programmes.

“While the chancellor announced in August and October 2016 that the government would guarantee EU projects agreed before we leave the EU, this is only applicable to those organisations who bid directly to the commission for funding.”

A Home Office spokesperson said: “The Government has guaranteed funding for organisations that successfully bid directly to the European Commission for Asylum, Migration and Integration Fund.

“We are committed to effective integration. In February 2019 we published the integrated communities action plan and committed to work with civil society and others to increase integration support for all refugees in the UK. Our focus is on supporting refugees with English language, employment and entrepreneurship, and wellbeing.”