The government’s settled status scheme for EU nationals living in the UK after Brexit risks creating “this generation’s Windrush”, a charity which runs a Home Office-supported project to help vulnerable people access the programme has warned.

With up to a third of the estimated 3.4 million UK-based EU nationals yet to apply for the new status, the Aire Centre warned of a “ticking time bomb” for businesses which rely on European staff who may lose their right to stay in the country.

Many EU workers appear to be holding back from submitting applications because they wrongly believe they will be rejected because they earn less than £30,000, warned the centre’s director Matthew Evans.

In fact the £30,000 minimum salary threshold currently applied to skilled migrants from outside the EU is set to be extended to new arrivals from the UK’s former European partners, not to those already here. And it is currently under review by the Migration Advisory Committee (MAC), due to report to Boris Johnson’s government by the end of this month.

If lower-paid EU workers miss the deadline to apply for the new status, they may never be allowed to work in the UK again, as they would be treated as new migrants below the salary threshold, said Mr Evans.

Bizarre: Boris Johnson drives 'Brexit' digger through boxes Show all 8 1 /8 Bizarre: Boris Johnson drives 'Brexit' digger through boxes Bizarre: Boris Johnson drives 'Brexit' digger through boxes Conservative party leader Boris Johnson drives a JCB through a fake wall POOL/AFP via Getty Images Bizarre: Boris Johnson drives 'Brexit' digger through boxes Prime Minister Boris Johnson during a visit to JCB cab manufacturing centre in Uttoxeter, while on the General Election campaign trail. PA Photo. Picture date: Tuesday December 10, 2019. See PA story POLITICS Election. Photo credit should read: Stefan Rousseau/PA Wire Stefan Rousseau PA Bizarre: Boris Johnson drives 'Brexit' digger through boxes Britain's Prime Minister and Conservative party leader Boris Johnson drives a Union flag-themed JCB, with the words "Get Brexit Done" inside the digger bucket, through a fake wall emblazoned with the word "GRIDLOCK", during a general election campaign event at JCB construction company in Uttoxeter, Staffordshire, on December 10, 2019. - Britain will go to the polls on December 12, 2019 to vote in a pre-Christmas general election. (Photo by Ben STANSALL / POOL / AFP) (Photo by BEN STANSALL/POOL/AFP via Getty Images) BEN STANSALL AFP via Getty Bizarre: Boris Johnson drives 'Brexit' digger through boxes Prime Minister Boris Johnson sits in a cab of a JCB during a visit to its cab manufacturing centre in Uttoxeter, while on the General Election campaign trail. PA Photo. Picture date: Tuesday December 10, 2019. See PA story POLITICS Election. Photo credit should read: Stefan Rousseau/PA Wire Stefan Rousseau PA Bizarre: Boris Johnson drives 'Brexit' digger through boxes Britain's Prime Minister and Conservative leader Boris Johnson drives a Union flag-themed JCB, with the words "Get Brexit Done" inside the digger bucket, through a fake wall emblazoned with the word "GRIDLOCK", during a general election campaign event at JCB construction company in Uttoxeter, Britain, December 10, 2019. Ben Stansall/AFP/Pool via REUTERS POOL REUTERS Bizarre: Boris Johnson drives 'Brexit' digger through boxes A sign made for a visit by Prime Minister Boris Johnson to the JCB cab manufacturing centre in Uttoxeter, while on the General Election campaign trail. PA Photo. Picture date: Tuesday December 10, 2019. See PA story POLITICS Election. Photo credit should read: Stefan Rousseau/PA Wire Stefan Rousseau PA Bizarre: Boris Johnson drives 'Brexit' digger through boxes Britain's Prime Minister and Conservative party leader Boris Johnson drives a Union flag-themed JCB, with the words "Get Brexit Done" inside the digger bucket, through a fake wall emblazoned with the word "GRIDLOCK", during a general election campaign event at JCB construction company in Uttoxeter, Staffordshire, on December 10, 2019. - Britain will go to the polls on December 12, 2019 to vote in a pre-Christmas general election. (Photo by Ben STANSALL / POOL / AFP) (Photo by BEN STANSALL/POOL/AFP via Getty Images) BEN STANSALL AFP via Getty Bizarre: Boris Johnson drives 'Brexit' digger through boxes Britain's Prime Minister and Conservative party leader Boris Johnson reacts as he sits in the cab of a drives a Union flag-themed JCB, after driving through a fake wall emblazoned with the word "GRIDLOCK", during a general election campaign event at JCB construction company in Uttoxeter, Staffordshire, on December 10, 2019. - Britain will go to the polls on December 12, 2019 to vote in a pre-Christmas general election. (Photo by Ben STANSALL / POOL / AFP) (Photo by BEN STANSALL/POOL/AFP via Getty Images) BEN STANSALL AFP via Getty

His warning came as a senior cancer researcher said scientific support staff from EU nations were already being put off applying for jobs in the UK because they fear they will be caught by the salary requirement.

“One of the first questions they ask me is ‘Is the UK still open to immigration?’” said Cancer Research chief clinician Prof Charles Swanton, describing the loss of skilled EU workers as “potentially catastrophic” to scientific work.

He told BBC Radio 4’s Today: “I see no justification for a salary threshold for highly skilled workers. We have some incredibly skilled workers who are paid a lot less than £30,000 a year.”

Speaking on the eve of Thursday’s publication of new Home Office statistics on the processing of applications for settled status, Mr Evans called on businesses to ensure that staff are helped to obtain settled status, which will allow people with more than five years’ residence in the UK to continue to live and work in the country after June 2021.

He warned of a “forgotten Brexit” for EU nationals who fail to register for the new status and are forced to leave the country or fall into a precarious life of undocumented work in the black economy.

“Businesses have an obligation to support their workforces and reach out through their supply chains to ensure that any EU staff and their dependants are helped through the scheme,” Mr Evans told a seminar in London. “The damage to British industry and the risks of thousands being forced into unemployment, or undocumented work and possibly modern slavery must not become the forgotten Brexit.”

And he added: “Brexit must not become this generation’s Windrush. History has shown us that promises made now are not always upheld later and we must act now to ensure EU nationals continue to be protected by their fundamental rights.”

The most recent Home Office statistics, released last month, showed nearly 2.6 million EU, EEA and Swiss citizens had applied for settled status by the end of November.

More than 2.2 million of the claims have been completed, with 59 per cent receiving settled status and 41 per cent “pre-settled status”, which allows them to remain in the UK until they have totted up a full five years’ residence before applying to switch to full settlement.

Despite a success rate of almost 100 per cent for those whose applications have been processed, Mr Evans said many EU nationals were believed to be putting off filling in their forms or to be unaware of what they need to do, with the vast majority thought to be in employment in the UK.

“The future salary threshold for EU nationals coming to work in post-Brexit Britain has been well publicised at a possible £30,000,” he said.

“For many, their income will fall below this level and understandably, they are worried about completing their applications for fear of being rejected. It is vital we debunk this myth, and employers take action to ensure their workers are guided through the settled status process to secure the status and rights that they are eligible for and to prevent disruption to business operations.”

With the future supply of EU workers at risk, the Aire Centre said it was even more vital for businesses to hold on to their current workforce, particularly as individuals from EU nations are likely to be over-qualified for the roles they have in the UK.

According to figures from Oxford University’s Migration Observatory, EU nationals make up 7 per cent of the UK labour market, with the figure rising to 21 per cent among low-skilled jobs in the factory and construction sectors. Retail and manufacturing are also particularly dependent on European staff, with 50 per cent of all EU nationals in the UK working in these industries.

Susan Banister of the Slave-Free Alliance warned that many people from mainland Europe are working in conditions of modern slavery in the UK, trying to pay off debts to organised crime groups, and risk missing out on settled status because they are unaware of their rights.

“It is in the gangs’ interests to not tell these people about their rights, especially the need to apply for EU settled status,” she told the meeting. “If they lost their legal status this makes them more vulnerable and more reliant on the traffickers. They are truly trapped in modern slavery.”

The Migration Observatory’s director Madeleine Sumption, said: “EU workers are employed right across the UK labour market, from science and research positions to low-wage factory jobs.

“More than half of highly-educated workers born in new EU member states were in low and medium low-skilled jobs in 2018. This means they are more likely to work in jobs for which they are over-qualified, one of the reasons EU citizens have been so attractive to UK employers. A range of industries have become quite dependent on this workforce.

“The government faces a big challenge getting all EU citizens through the settlement scheme.

“Regardless of how easy it is to apply and how well the scheme is communicated, there will inevitably be people who simply don’t realise that they have to do it.

“This challenge is compounded by the fact that there are no accurate figures on how many people are eligible to apply: the most commonly used estimate of 3.4 million is almost certainly too low. So it’s possible that hundreds of thousands of EU citizens could fail to apply without this being clear from the data.

“One of the big questions for the next couple of years will therefore be whether the deadline is extended or, as some have suggested, removed entirely.”

Mr Evans said: “The contribution EU workers make to the UK economy and to business is unquestioned, but many are put off by the red tape and complicated process. Businesses need to take action now, and failing to do this is tantamount to ignoring a ticking time bomb on a boardroom table.”

A Downing Street spokesperson said that MAC had been asked to review the salary threshold for future migrants, adding: “The prime minister has made clear we want to be welcoming to immigrants and want to attract the brightest and best to the UK.”

A Home Office spokesperson said: “These comments, made by an organisation we fund to support EU citizens, are quite simply wrong.

“The government has made it repeatedly clear that we want EU citizens to stay, and 2.5 million people have been granted status already.