Tens of thousands of EU citizens resident in the UK – including some of the “heroes and heroines of the coronavirus crisis” – could be facing deportation because they have fallen through the cracks of the government’s post-Brexit settled status scheme, a group of MPs has warned.

The MPs have written to Boris Johnson calling for a legal “right to stay” to provide reassurance to more than 3 million EU nationals believed to be living in the UK.

Under the government scheme, nationals of the EU, EEA and Switzerland who have been in the UK continuously for five years can apply for settled status allowing them to remain, while others who came to the country before the end of 2020 can get “pre-settled” status which can be upgraded once they reach the five-year mark.

By the end of July, some 3.8m applications had been made and 3.6m concluded, with just over 2m people – 57 per cent of applicants – being granted settled status, 1.5m (41 per cent) pre-settled status and around 75,000 (2 per cent) classed as refused, withdrawn, void or invalid.

Signatories to the letter said the figures showed that hundreds of thousands of people would be left for up to five years after the end of the Brexit transition period in December before knowing whether they will be able to stay long-term. And they said that, even if the scheme was 98 or 99 per cent successful, the number without the right to remain at the end of 2020 could stretch into tens of thousands.

The letter, signed by Scottish National Party Westminster leader Ian Blackford, Liberal Democrat home affairs spokesman Alistair Carmichael, Plaid Cymru leader Adam Price, SDLP leader Colum Eastwood and Green MP Caroline Lucas, noted that migrants make up a large proportion of the delivery drivers, agricultural workers, supermarket staff, nurses and care home workers who kept the country running during the coronavirus lockdown.

“It should be a matter of national shame that many of the heroes and heroines of the coronavirus crisis will have been made to feel so unwelcome in this country by the tone and content of our national debate on immigration,” said the MPs.  

“Millions of European migrants who live in the UK and who are now working in hospitals and supermarkets derive their right to be here from EU freedom of movement rules which the government is seeking to abolish. They are now being asked to apply for their right to stay in the UK via the settled status scheme, a process which is not guaranteed to be successful.  

“Although settled status has now been granted to many EU citizens, we are extremely concerned at the prospect of some losing their status in the UK. With much of the government and third sector having been shut down by the coronavirus crisis, the applications system has been severely disrupted, as has the support system for applicants and public awareness campaigns. Unless the government acts, many thousands of people could fall through the cracks.”

They called on Mr Johnson to pass primary legislation to grant a legal right to stay to EU citizens.

Mr Blackford said: “The UK government must confirm the rights of EU nationals to remain as a matter of urgency.  

“Many people risk falling through the cracks, causing uncertainty and distress for thousands of EU nationals who have made the UK their home.”

And Ms Lucas added: “The millions of EU citizens who have made their home in the UK are not just a statistic, or an economic asset – they are our neighbours, friends and families. The idea that we could allow any one of them to lose their status here should fill us with shame.

“Yet that is inevitably what will happen to thousands of people unless the settled status system is fundamentally overhauled, even if the overwhelming majority do apply successfully.  

“During the EU referendum, those campaigning for Leave said that Europeans living in the UK would have a right to stay, not a right to apply to a convoluted system which might reject them. Today, we are asking that this very basic promise be honoured.”

Alena Ivanova, an organiser for the Right to Stay and Another Europe is Possible campaigns, said that the UK government had so far failed to guarantee that absences from Britain during the coronavirus crisis – when some EU nationals have been trapped abroad for lengthy periods – would not count against an applicant’s claim to have been in the country for five unbroken years.

“While the Home Office paints a rosy picture of the success of the settlement scheme, there are still millions at risk of losing their rights in the coming years,” she said.

“A system that asks you to apply to stay in your home – in some cases twice – is not what European nationals were promised.

“Even if we assume that 98 or 99 per cent of them apply successfully that would still mean tens of thousands of people facing deportation from the place they have made their home.

“Since coronavirus struck, we have had a plethora of reports of new issues which simply cannot be overcome in time – from a lack of awareness and support in the application process to periods of absence from the UK during the crisis. It’s time for the Home Office to re-assess the scheme and grant automatic status to all.”

A Home Office spokesperson said: “The EU settlement scheme makes it easy for EU citizens and their family members who want to stay in the UK to get the immigration status they need. It provides them with secure evidence which they can use to demonstrate their right to work, study, housing and benefits.

“There have been more than 3.8 million applications to the EU settlement scheme already and more than 3.5 million grants of status. People’s rights are secured in UK law whether they have pre-settled status or settled status.”