Thousands of applications made to the EU Settlement Scheme by people asking for the right to remain in the UK after Brexit have been unsuccessful, figures suggest.

The Home Office said so far just two applications have been refused on “suitability grounds”.

But analysis by the PA news agency of the department’s figures indicate around 7,600 applications did not result in people being granted full permanent permission to live and work in the UK – called settled status – or temporary leave to remain, known as pre-settled status.

The news prompted concerns from campaigners and immigration lawyers who fear EU citizens and their families could be put at risk of deportation if they are not granted leaver to remain before the deadline.

They claim the publication of “select figures” is “disingenuous” and could give a “misleading” impression that the scheme is successful.

EU citizens and their relatives – including those from the European Economic Area (EEA) countries of Iceland, Liechtenstein and Norway as well as Switzerland – have been asked to apply to confirm their immigration status so they can live and work in the UK when freedom of movement ends.

Relatives of EEA and Swiss citizens who are not from any of those countries but all currently live in the UK under EU law are also being urged to apply.

Once granted status, applicants can use the NHS, study and access public funds and benefits, as well as travel in and out of the country. But first they must prove their identity, show they live in the UK and declare any criminal convictions before a December 2020 deadline.

Overall, the total number of applications finalised by the end of September was more than 1.5 million (1,524,500).

Of these, 61% were granted settled status and 38% were given pre-settled status – which can be applied to be updated once someone has lived in the country continuously for five years – while the conclusion in 0.5% of cases was classed as having “other outcomes”.

The data says cases with other outcomes include applications not granted leave to remain because it was deemed: “invalid” as mandatory information was not provided; “void” because the applicant was ineligible; was “refused on eligibility or suitability grounds”; or the applicant withdrew the application.

Those who were branded ineligible could include people who were already found to be a British citizen, the research said.

The Home Office has been contacted for comment and asked to provide a full breakdown of the figures.

All the statistics published were branded experimental and should be “treated with caution”, the department warned, adding that percentages may not add up to 100 due to rounding of numbers.

Maike Bohn, co-founder of campaign group the3million, told PA: “The figures are disingenuous and self-serving as they are trying show the scheme is going well.

“The Government is hiding behind formalities and soundbites. The devil is in the detail.”

She claimed the Home Office could be “hiding refusals” by recording decisions which ultimately constituted this under different headings, adding: “It is very select data so we cannot clearly know.”

Zeena Luchowa, an immigration solicitor at Laura Devine Law, told PA large numbers of people were seeking legal advice on the scheme because they had found the process confusing, adding: “There’s a real concern as to what exactly is going on at the Home Office and the types of decisions that are being made.

“What is worrying is trying to find out what is happening when there are rejections.

“Being rejected doesn’t mean the application has been refused but it still has ramifications.”

She said the scheme did not appear to be as straightforward as intended.

More than 1.8 million people had applied by the end of September, according to the statistics. But the latest internal figures show a total of two million applications, the Home Office said.

There were an estimated 3.6 million EU citizens living in the UK in 2018, but that number could be nearer four million now, data and research by immigration experts indicates.

In August, the Office for National Statistics admitted it had underestimated EU net migration to the UK and the figures could be higher than first thought.

Earlier this year, the scheme came under fire when a chef who has twice cooked for the Royal family was denied settled status despite saying he had proof of living in the UK for almost 15 years.

Damian Wawrzyniak, 39, said he provided employment and tax documents but was denied unconditional permission to stay in the country he now calls home indefinitely.

Instead he was granted pre-settled status which means he will be later forced to re-apply for full settled status.

The Government insisted the scheme was “performing well” and said they had contacted Mr Wawrzyniak for more information.

Last week, Yvette Cooper, chairman of the Commons Home Affairs Committee, wrote to Home Secretary Priti Patel asking her to provide “accurate information” because there was “still a lack of clarity” over some aspects of the scheme.

The Advertising Standards Authority (ASA) has also banned a radio advert for the scheme for failing to make clear documents as well as a passport or ID card would be needed to apply – a decision the Home Office said it completely disagreed with.