A UK Government pilot scheme to register the estimated 3.5 million European nationals who live in the UK and want to remain post-Brexit could create a scandal “worse than Windrush” according to a leading charity.

Under the scheme, which starts today, those who register to remain beyond June 2021 will have to pay £65 (£32.50 for children) to apply for “settled status”.

However, it is feared that many could end up like some members of the Windrush generation, who were wrongly targeted for immigration enforcement – removal – when they could not prove their status.

The Joint Council for the Welfare of Immigrants (JCWI) said in a statement: “The Home Office doesn’t have the best track record, let’s be honest and we are very worried about vulnerable groups simply falling through the cracks – the hostile environment meanwhile continues unabated. We don’t want anyone to be put off applying through the pilot scheme – in fact, we want people to know about it and register.

“But by making EU nationals apply for a new status, and also pay a fee, the government is guaranteeing that even if the system is simple and works well for 95% or 99% of EU nationals, there will be tens of thousands of people currently living in the UK left undocumented, without legal status, and exposed to the hostile environment.

“It’s going to be much worse than Windrush.”

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The JCWI said the government should fix this by giving all European Economic Area (EEA) nationals, their families and others with rights to reside under the treaties, automatic permanent settled status as a right.

It could also allow them to register and give them documentation proving that status free of charge using the simple process similar to the one they have already developed.

“This would mean that everyone the government has promised would be allowed to stay would have the legal right to do so, without having to make an application, but could still obtain documents to prove their status quickly and easily,” said the charity.

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Jill Rutter, strategy director of think tank British Future, said: “The Home Office must invest in getting the EU settlement scheme right from the start.

“Failure to do so could cause massive problems in years to come, on a far bigger scale than the Windrush scandal.”

Immigration Minister Caroline Nokes said extensive testing “shows clearly that we are well on track to deliver a system that will make it easy and straightforward for EU citizens to obtain status”.

However, pressure group the3million surveyed its EU members who said their biggest concern was losing rights in the future. Founder Maike Bohn warned that trust in ministers is low: “The Windrush people trusted the Home Office and many of them got deported because they were citizens but couldn’t prove it.”

Officials said they expect to process about 6000 applications a day, with about 1500 caseworkers on the scheme and a further 400 in a resolution centre to deal with issues.

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A trial of almost 30,000 applicants was restricted to people in specific professions, with only a small number of vulnerable people taking part. More than two thirds were approved in three working days and 81% within a week.

While improvements have been made, nearly a quarter of people told the government they found it difficult during previous testing.

A Home Office spokesperson said: “It will be simple and straightforward for EU citizens to get the status they need. They will only need to complete three key steps, prove their identity, show that that they live in the UK, and declare any criminal convictions.”