One of the UK’s most prestigious universities has seen its funding from a large European research programme plummet from £62m a year to nothing since Brexit, new figures show.

The latest statistics from the European Commission reveal that Cambridge University, which netted €483m (£433m) over the seven years of the last European research funding programme, Horizon 2020, has not received any funding in the first two years of the new Horizon Europe programme.

Meanwhile, Oxford, which won €523m from the earlier programme, has only been awarded €2m to date from Horizon Europe.

Britain’s associate membership of the €95.5bn Horizon Europe programme was agreed in principle as part of the Brexit trade deal negotiations in 2020, but ratification was disrupted after the UK failed to implement the Northern Ireland protocol. Such funding is vital to UK universities because it enables research collaborations with institutions across Europe and carries considerable international prestige.

“For higher education and research, there are no new opportunities and no actual possible upsides from Brexit,” said Simon Marginson, professor of higher education at Oxford.

He described Brexit as a “historic error of monumental proportions” and said the new data on Oxford and Cambridge – usually the top performers in Europe – was “very worrying”. The losses reached beyond money, he added, with the UK also becoming less attractive to high-quality European researchers and students.

The government has guaranteed it will cover all successful Horizon Europe grants applied for by the end of March, but after watching the political wranglings for more than two years, many academics are now leaving the UK, saying they no longer believe their vital European research partnerships will be protected.

In August last year, Professor Augusta McMahon, an archaeologist specialising in the Middle East, left Cambridge University, where she had worked for 26 years, to return to Chicago University. Although she was wooed to the US by what she calls “the best job in my field”, she says Brexit uncertainty was a big factor. “I no longer thought the government would either associate [with Horizon Europe] or provide replacement funding,” she said.

With the number of EU students coming to UK universities more than halving since Brexit, she was noticing their decline on campus. Meanwhile, she said fewer European lecturers were applying for jobs here.

Professor Paul Pharoah, who researches the genetic epidemiology of ovarian and breast cancer, left Cambridge after 26 years at the end of last year and now works at Cedars Sinai hospital in Los Angeles.

Pharoah, who was involved in two large EU-funded research projects in the past 15 years, said it was becoming much harder to find funding for his field in the UK: “And the lack of opportunity to apply for EU funding made the outlook even more bleak.”

Gáspár Jékely, a German professor of neuroscience who was based at Exeter University, started work at Heidelberg University last week. He has taken his high-cachet European Research Council (ERC) advanced grant with him.

“The lack of security around European collaborations and funding was one of my reasons for going,” he said. “Recruiting researchers and post-docs from Europe was becoming increasingly hard.” He added: “A colleague of mine at Exeter has just won a prestigious ERC grant, but we don’t know what will happen with it. No one wants to lose a €3m award.”

Last April, the ERC gave 150 grant winners in the UK two months to decide whether to move with their grant to a European institution or lose the funding. In the end, UK Research and Innovation, the government research funding organisation, matched the funding of those who stayed, but one in eight left the UK.

Vassiliki Papatsiba, an education expert at Cardiff University who has researched the impact of Brexit on universities, said the UK might continue to lose talented researchers this way. “Nearly 50% of ERC UK-based grant winners are nationals of a different country, so that would predispose them to outward mobility,” she said.