Britain’s universities are already seeing a fall in their share of a crucial pot of European Union funding, with vice-chancellors fearing that UK projects are losing out even before Brexit has taken place.

Millions of pounds to pay for crucial research has been lost as a result of a fall overall in Britain’s share of the flagship Horizon 2020 project, a £70bn fund aimed at cutting-edge science.

Official figures reveal a downturn in both UK participation in, and funding from, the project. University sources said that while there were sometimes natural fluctuations in which countries received money, there was now a “downward trend across several key indicators over the past 18 months”.

There are concerns that Brussels is reluctant to fund UK-based projects, despite the government’s pledge to underwrite scientific research funding once Britain has officially left the bloc.

From February to September last year, the proportion of UK participation in the project was 15% of the total, while it took just under 16% of the share of funding, according to government figures compiled by Universities UK. Over the same period this year, UK participation fell to 12% and funding fell to 13%.

The impact is being felt most keenly in the part of the programme that funds projects looking at “societal challenges”. The UK’s share of funding in that area is down more than three percentage points in the last quarter.

Alistair Jarvis, chief executive of Universities UK, said the downturn in participation in the programme was concerning. “It highlights the urgent need for clarity on the UK’s participation in Horizon 2020 beyond Brexit and, while the UK is still a member of the EU, the need to communicate that the UK’s universities and researchers are still eligible to participate and apply for funding through EU research and innovation programmes.

“The UK benefits enormously from the access to vital networks, funding and talent Horizon 2020 provides. It allows researchers to collaborate with world-leading experts on life-changing research, with knock-on benefits for the economy, society and individuals in the UK.”

Labour said that the UK’s share of funding from Horizon 2020 had fallen by more than £100m in the year to September and that the party had been contacted by vice-chancellors with concerns. They asked for their comments to remain anonymous.

“Our researchers applying for European funding need to know what will happen to their grant applications if they’re not fully signed off by the time we leave the EU,” said one. “The danger is that our plans for important research could hit the buffers.”

Another said: “It is so frustrating watching the country head towards a potential barren land for research. There seems to be a lack of understanding that developing and securing funding for research proposals can take up to 18 months. Life-changing medical, scientific and technological research will be delayed unless we get assurances soon.”

Paul Blomfield, shadow Brexit minister, said: “Ministers need to recognise the damage that their flawed approach to the Brexit negotiations is doing and act quickly to secure our future in European research programmes.”

A spokesperson for the Department for Business, Energy and Industrial Strategy said: “The UK remains one of the strongest participants in Horizon 2020. The European commission has made it clear that proposals from, or including, UK applicants must be treated in the same way while the UK is a member of the EU, and we encourage UK researchers, scientists and businesses to continue applying for funding.

“The government has been clear in its commitment to the UK’s world-leading science and research base. Through our new industrial strategy we are investing a record further £2.3bn in R&D to secure our status as a pioneering nation, and will discuss an ambitious science and innovation agreement with the EU to continue our successful partnership.”

There continues to be widespread anxiety among EU nationals working in UK education about their status after Brexit. According to the latest data, 17% (33,735) of academic staff and 6% (12,490) of professional services staff at UK universities are from other EU countries.

Meanwhile, the number of EU nationals training as teachers in Britain has fallen for the first time in six years, according to data compiled by the Lib Dems. There were 4,690 qualified teachers from the European Economic Area in 2016-17, down slightly from 4,795 the previous year. The number of teachers from Poland saw a significant fall of 12%, from 545 to 481.