Quarterly figures issued on Thursday showed just over 6.1m applications had been received for the scheme that gives EU citizens, EEA nationals and their families the right to live, work, study or retire in the UK if they were in the country at the time of the EU referendum in 2016.
But it transpires that 470,000 of those were repeat applications, meaning the total number of applicants was closer to 5.5m by the cut off date of 30 June.
However, the figures also lay bare the scale of the task still facing case workers at the Home Office. By the end of June 4.9 million had been granted status, leaving a huge backlog of just under 660,000.
Home Office figures for August show that backlog is now down to 450,000 suggesting the government is processing about 100,000 applications a month.
This puts it on course to clear the backlog by the new year.
While the settlement scheme has been hailed as a huge success, four in 10 will find themselves facing the Home Office process all over again when the five-year clock on their pre-settled status stops ticking and they can apply for settled status.
But it means that nearly 5 million people have been granted status to continue living and working in the UK in the clearest picture so far of the status of EU citizens in the country. Of the 6m applications, just over 1m were made on behalf of children.
The immigration minister, Kevin Foster, said on Thursday that it would still accept late applications for EU settled status, accepting that some may not have been aware that they needed to do so.
He said: “I’m delighted thousands more people have been rightly granted status through the hugely successful EU settlement scheme. We continue to work as quickly as possible to conclude applications, as well as supporting people with their late applications.
“Our message remains clear. The Home Office is looking for reasons to grant status rather than refuse. I would encourage anyone eligible who is yet to apply to get in touch and join the millions who have already secured their rights.”
The Home Office still faces criticism over huge delays in processing applications from the EU spouses of British citizens who want to return from the EU.
There is also anecdotal evidence of delays in issuing the certificate of application which can be used to prove the right to remain in the UK while cases are pending.