EU citizens who have been in the UK for fewer than five years and apply to remain in the UK after Brexit face further uncertainty because of a flaw in the Home Office phone app, it has emerged.

A 31-year-old Swedish engineer who has applied to stay in Britain after Brexit discovered the defect in the app when he tried to convert his pre-settled status to settled status last week.

Hugo Nilsson came to the UK in July 2014 and would have been eligible for full settled status this month, but was so anxious about his future in the country that he jumped at the chance to try to secure his rights as soon as he could.

When the Home Office opened the national scheme for EU citizen residency rights in April, he applied for what is known as “pre-settled status”, a legal status created by the Home Office for those who have been in the country for fewer than five years but envisage remaining for longer.

“I applied in April. I didn’t want to wait until July for full settled status just for peace of mind,” said Nilsson.

But when he reached his fifth anniversary on 5 July this year, “the computer said no” and he was told that it was not technically possible to apply to convert his pre-settled status into settled status.

“I phoned the helpline and asked to speak to the supervisor of the team, and I was told they had not rolled out the functionality yet. I asked them when they would be doing that, and they said they did not know,” he said.

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He said he felt the Home Office technology had now inadvertently derailed his plans to apply for citizenship in August, which would cement his status in the UK in the event of a no-deal Brexit.

“I feel that they knew this when they launched the app and they should have had a warning saying, ‘If you think you will be eligible for settled status shortly, you should hold off applying for settled status as you won’t be able to convert it,” said Nilsson.

The Home Office admitted the existence of the flaw, but said it hoped the functionality would be available within weeks.

“Mr Nilsson is one of almost 700,000 people who have already secured status through the EU Settlement Scheme. From the end of July, it will be possible for people with pre-settled status to convert to settled status as soon as they become eligible,” said a spokesman.

It is not the first technical flaw in the app. The Home Office had to admit it would only work on Android phones and not iPhones when a pilot scheme was launched last August. Apple is making the technology available to the Home Office this autumn to rectify this.

Nilsson acknowledges the achievements of the Home Office in getting a new immigration app up and running in the short time it had, but said it should have communicated the shortcomings to applicants from the beginning.

He also thinks the customer service centre should have been informed of the timeline and not just said they “didn’t know” when the functionality to convert status would be available.