More than a quarter of EU citizens are having their applications for permanent residency in the UK rejected since the UK voted to leave the EU, according to new analysis of the government’s migration data.

If the government was to require all EU citizens to apply for permanent residency, the refusal rate could mean 800,000 EU citizens are left without certainty as to whether they can stay in the UK post-Brexit, according to the research.

In the last two quarters of 2016, more than 12,800 EU citizens had their permanent residency requests refused with a further 5,500 declared invalid, a rejection rate of around 28%, analysis by the Liberal Democrats found. To qualify, EU nationals need five years of continued residence in the UK.

Article 50 day won't be cut-off date for EU migrants, No 10 suggests Read more

The day that Theresa May triggers article 50 next month is reported to be the most likely cut-off date for when EU citizens will no longer have the automatic right to stay in the UK, with the prime minister prepared to guarantee that those here before that date will be protected as long as UK citizens in Europe have reciprocal rights.

Depending on how long the tussle between the Lords and the Commons goes on before the article 50 bill receives royal assent, May will still comfortably meet her self-imposed end of March deadline and is likely to trigger the formal two-year process for leaving the EU by about 20 March.

Former cabinet minister Iain Duncan Smith told the Telegraph the statement would mean she “commands the high ground”. It is thought that the government could be at risk of legal challenge if May attempted to make 23 June last year, the date of the referendum, the cut-off date.



Government sources said nothing had been finalised with regards to EU citizens’ rights post-Brexit or any cut-off date, but did not deny the mooted date of the triggering of article 50 was a possibility.

The home secretary, Amber Rudd, repeated the pledge that the government “will be ending freedom of movement as we know it” but said she would not expect immigration to fall dramatically immediately after the UK leaves the EU, echoing comments by the Brexit secretary, David Davis.

Last week, the quarterly migration statistics from the Office for National Statistics showed there had been a doubling of the number of EU nationals in Britain who had their applications processed for UK residence documents to secure their individual status.

Rudd said the government was “against cliff edges” when it came to reducing immigration. Ministers are reported to be considering a five-year working visa whose holders would be banned from claiming benefits, according to the Sunday Times.

A Home Office spokesperson said the refusal rates included applications that were invalid because of errors or unpaid fees and said that meant it would be “wrong to draw conclusions” about the reasons for the rejections.

“Refusal rates have not changed over the last year,” the spokesman said. “European citizens resident in the UK make a vital contribution both to our economy and our society. That’s why we will be making securing their status, as well as that of British nationals in the EU, a priority as soon as we trigger article 50 and the negotiations begin.

“EEA nationals are not required to apply to the Home Office for documentation confirming their status or their right to be here and these rights remain unchanged while we are a member of the European Union.”

The home secretary has previously been thought to prefer a permit system. Speaking to ITV1’s Peston on Sunday, Rudd said that was one of a number of options which would be considered, as well as a work permit system where the government would control how many EU citizens could enter the UK every year to take up a job offer with a UK company.

Rudd confirmed that the government would consult businesses over plans for an immigration system over the summer. ”We’re looking at all sorts of different alternatives,” she said.

May has in effect ruled out a points-based system, which was the stated preferred option of the Vote Leave campaign, including Boris Johnson and Michael Gove.

Davis said last week that it would take “years and years” for UK businesses and the NHS to replace EU staff in areas such as hospitality and social care. “Don’t expect just because we’re changing who makes the decision on the policy, the door will suddenly shut: it won’t,” he said during a visit to Estonia.

Rudd said Davis had been highlighting “the fact that as a government we’re going to work with businesses, with employers, to make sure that the immigration system we put in place does enable them to continue to thrive and continue to grow”.

However, the Conservative party chairman, Sir Patrick McLoughlin, insisted the government was still committed to reducing numbers, saying Davis’s comments had been taken out of context. “We have the figures towards the end of last week which have shown a reduction [in] net immigration to the country … so I think we need to see how that was done,” he said.

“David is very committed to the prime minister’s agenda, and that is actually ensuring that we get control over our own borders, which was one of the biggest issues in the referendum.”

The House of Lords is likely to back amendments to the article 50 bill this week that would guarantee rights to EU citizens, with support from Labour, Liberal Democrat and crossbench peers. More than 80 peers across the parties voiced concern for the rights of EU nationals over the course of the two-day debate at the bill’s second reading in the Lords.

The Lib Dem foreign affairs spokesman, Tom Brake, said the numbers of EU citizens who were being left with no guarantees about their future was unacceptable. “Our prime minister must provide certainty now for the EU citizens who work in our hospitals, care homes, schools and factories,” he said.

“Amber Rudd is talking about a consultation with business this summer. That is not good enough. It is disgraceful to leave people in limbo till then. This government have no shame.”

Rudd hit back at reports criticising the government for its decision to end the scheme to bring unaccompanied refugee children from camps in Europe to the UK, saying it was “fake news” that the UK was shutting the door.

Campaigners voiced anger after the government said it would take no more than 350 children as part of its commitment to the Dubs amendment, put down by the Labour peer Alf Dubs. It was widely understood at the time the amendment was accepted that the government would take about 3,000 unaccompanied minors from the camps in Europe, including Calais.

Rudd denied Lord Dubs and others had been misled. “Every word was haggled over and decided over last year, that there would be a consultation with councils and we would come back with a number, that it would be a one-off system,” she said. “What happened in Calais is the number of children doubled over three weeks. If you set up a system of taking children from Europe, the traffickers will bring you the children.”

Labour MP Yvette Cooper, chair of the home affairs select committee, has disputed Rudd’s claims, saying her committee had heard from several charities that the closure of the Dubs scheme was giving traffickers an incentive to offer children illegal routes into the UK, rather than waiting for safe and legal routes.

• This article was amended on 27 February 2017. An earlier version said that in the last two quarters of 2016, more than 800 EU citizens had permanent residency requests refused. That figure has been corrected to 12,800.