After eight years researching music history at Glasgow University, Elizabeth Ford hoped her request for a visa extension would sail through this summer. Instead, the Home Office gave the American academic two weeks to pack up her life and leave the country.

Ford has held a research fellowship at Edinburgh University – which, like Glasgow is in the elite Russell Group – and is due to begin a new research fellowship at Oxford University. But this is in jeopardy after a letter from the Home Office in July, which said that her leave to remain, granted a year before, was erroneous, and that she must leave within two weeks.

Ford, an expert on 18th century Scottish music, who says she loved Scotland from the moment she first set foot there, says: “After eight years I had 14 days to get out. It was truly shocking. I have never felt so unwelcome or so offended.”

Ford’s case adds to a growing storm over the visa system. While the government has announced plans to offer two-year work visas for international students, nothing similar has been offered to researchers from abroad, who say the process is hostile, cumbersome and punitively expensive. University leaders say the situation could block the talent pipeline to the UK.

Ford is refusing to leave her home in Glasgow and has been strongly backed by Scottish MPs, including Ian Blackford, the Scottish National party’s Westminster leader. She has consulted immigration lawyers who say she has a case to appeal on human rights grounds.

She came to Glasgow to do her PhD under a student visa, then obtained a doctoral extension visa for a year. The research fellowships she has won since do not come with a fixed employment contract, so a charity sponsored her last visa applications. “The visa system in the UK is completely arcane and arbitrary,” she says. “It is focused on high income and nothing else. But it is unrealistic to expect newly minted PhDs to find a permanent academic job with a high salary. It just doesn’t happen.”

Prof Roibeard Ó Maolalaigh, vice-principal and head of the college of arts at Glasgow, says Ford is a “valued colleague” and the university is very supportive of her application for a visa extension. “This case has caused considerable distress to Dr Ford, especially as it would appear that the issue was caused by an error at the Home Office,” he says.

Shamit Shrivastava, a post-doctoral research associate at Oxford University’s Institute of Biomedical Engineering, is forced to renew his visa every year at great expense.

However, it is not only academics who have had their visas refused who are unhappy. The cost of applying for a visa has increased considerably in recent years, and many young researchers are struggling to pay the fees. Dr Jana Bacevic, a sociology research associate on a part-time contract at Cambridge University, earns £1,200 a month. Last month she was horrified to hear that she had to pay £1,500 to cover the costs of extending her visa for a year while she looked for a permanent academic job. She tweeted: “You know what UK? Good night and good luck. I used to love this place with all its flaws, but hey, there are universities on the continent too.”

Gareth Edwards, an Australian who is a senior lecturer in human geography at the University of East Anglia, says: “If I was arriving today as a fresh postdoc I couldn’t finance it, especially with a family.”

Edwards, who has co-founded an academic campaign group called International and Broke, says a postdoctoral researcher with a three-year contract, a partner and two children on the average salary is now expected to pay more than 30% of their first year’s take-home pay – £7,240 – upfront on visa and immigration costs.

He says junior academics are hit hardest as they are often on short-term contracts and have to reapply for their visa – and pay thousands again – every time their contract is extended or they move jobs.

One young Indian academic, who asked not to be named in case it prejudices his future visa applications, says the costs felt overwhelming, coming to Liverpool University from Mumbai with his wife and baby. “I had visa costs of around £2,500. We had to use my father’s retirement savings,” he says.

Shamit Shrivastava, a post-doctoral research associate at Oxford University’s Institute of Biomedical Engineering, has had to reapply for his visa every year since he arrived in 2015. He says he is lucky because Oxford, unlike many other universities, pays the fees. But he still usually ends up spending hundreds more on the premium service each year to speed things up, because, typically, applications take two and a half months to process, meaning he could not work.

“When I first applied, the programme I was working for had the funding to employ me for at least three years but I was only given a one-year visa. It is very stressful to have to go through it all again every summer,” he says.

Shrivastava adds that to take out a loan or rent a flat for 12 months you need a visa of at least a year. This means that even a month after his paperwork is finalised, he is ineligible. “I only manage because I have a wife who is employed, but colleagues have really struggled with this,” he says. “The system leaves you with a feeling of helplessness.”

Martin Smith, policy manager at the Wellcome Trust, says UK visa costs for scientists are more expensive than competitor countries “by a long way”. The charity has also collected around 100 examples of cases where scientists wishing to come to the UK for conferences have had their visa declined unfairly. “These are disproportionately from lower-income countries, especially in Africa,” he says. “They are told they do not have sufficient finances, even if the trip is fully funded.”

Smith adds that the suspension of parliament means that the immigration bill making its way through Westminster has died and will need to be reintroduced in a new session. The trust is worried that there is no clarity about what the government intends to do on immigration. “It’s not reassuring for researchers right now,” he says. “For people thinking about moving their lives to another country it is an enormous decision.

“The current immigration system is so bad for science that unless we get some real clarity and improvement, talented people will drift away.”

A spokesperson for the Home Office says: “We welcome international academics and recognise their contribution to the UK’s world-leading education sector. All immigration applications are considered on their individual merits and on the basis of the evidence available.”