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US academics have warned that the Trump administration’s efforts to slash billions of dollars from university research budgets will erode the country’s competitiveness and reputation.

Their concern comes ahead of a deadline on Wednesday for Columbia to meet demands from the federal government to impose wide-ranging governance changes as a precondition for future funding.

Universities are already being forced to reduce spending and staff in response to the cuts.

Johns Hopkins University decided last week to eliminate nearly 2,000 jobs following the cancellation of $800mn in grants from the now-gutted US Agency for International Development.

“It’s like watching a train derail in slow motion knowing that the consequences will be quite catastrophic for our university and our researchers,” said Judd Walson, the university’s chair of international health.

“This is going to mark a very substantial collapse in public health and research that will have generational impacts.”

Like other universities, Johns Hopkins has faced the cancellation of grants that the Trump administration claimed were associated with diversity, equity and inclusion (DEI) policies it opposes and is threatened with penalties for alleged failure to tackle antisemitism on campus.

It will also be affected by the administration’s plan to cap funding for project overheads from the National Institutes of Health (NIH) to 15 per cent, although the cut has been temporarily blocked by a judge. Another lawsuit is challenging the cancellation of DEI projects.

Johns Hopkins is particularly vulnerable because of its long-standing links to the federal government for research — it is one of the largest recipients, with $2.8bn in funding last year — and its concentration on research and implementation of international health programmes, which were all but destroyed by the decision to scrap USAID.

It estimates that the threatened cut to NIH overhead support alone could cost it a further $200mn a year.

Because of the cuts Walson, like many of his peers across academia, has cut the number of PhD places his department is offering this year. “It’s created a huge leak in our pipeline,” he said.

Columbia University, one of at least ten universities under investigation by the Department of Justice, this month had $400mn in federal grants pulled in response to what the Trump administration claimed was its failure to address antisemitism.

Duke University estimates it will face a $200mn annual hit from the NIH cap alone, and has placed a freeze on most new hires and cancelled expenses ranging from construction to travel and entertainment.

Jenny Lodge, Duke’s vice-president for innovation and research, said: “It’s been just one thing after another, and we still don’t know what the final impact will be. We are hoping for the best but planning for the worst.”

She said fewer students will be recruited this year to graduate programmes and warned: “This gives more junior colleagues a lot of pause about whether being in academic research is a good thing.”

Meanwhile, staff cuts at federal agencies including the NIH and the Department of Education have left universities without interlocutors to whom they can appeal, seek clarification or advance the processing of grants approved or under review. That is causing delays with long-term consequences that will remain even if some policies are reversed or threats not carried out.

“There is no sign of a return to the status quo,” said Andrew Read, a senior vice-president for research at Pennsylvania State University. He added that the cuts will have an effect on local employment and economies in the areas where universities are based.

“This is kneecapping ourselves in R&D. American exceptionalism has been about incredible technological and scientific progress. You can’t just turn it off and turn it back on in two years.”

Others are more sanguine. “Research universities have received billions of dollars from the federal government and they should not have taken it for granted by discriminating in ways that disqualify them,” said Adam Kissel, a deputy assistant education secretary during the first Trump presidency and a visiting fellow at the right-wing Heritage Foundation think-tank.

He argued that institutions should be cutting administrative costs and dipping into their endowments to make good on any shortfalls in funding. “I’m not very sympathetic to universities that are wealthy but do not use their own money at least temporarily,” he added.

Todd Wolfson, president of the American Association of University Professors, warned that many higher education leaders were not speaking out or resisting for fear of being targeted.

“People have to stand up right now. I understand their fear but that looks from the outside like capitulation,” he said. “We know complicity with authoritarianism doesn’t work.”