Nearly five million people have been allowed to continue living and working in the UK under the EU Settlement Scheme so far, according to the latest official estimates.

Home Office figures show that, as of the end of June, 4,908,760 people had been granted an immigration status to remain in the country after freedom of movement ended following the Brexit transition period.

EU citizens – as well as people from Iceland, Liechtenstein, Norway and Switzerland – and their families had been asked to apply to the scheme by the June 30 deadline.

Quarterly data published on Thursday suggest more than 5.5 million people (5,548,440) had applied by that date.

This provides the clearest picture so far of how many people applied to the scheme by the closing date, as opposed to how many applications had been received. However, the Home Office data is listed as “experimental”, meaning the numbers are still being evaluated and may be revised in future.

The figures are far higher than the latest official estimate of how many EU nationals are living in the UK. The Office for National Statistics (ONS) indicated that in mid-2020 this was 3.5 million.

More than six million applications (6,050,860) were submitted between the launch of the scheme in March 2019 and the June 30 2021 cut-off date.

Some 2.8 million were granted settled status, allowing them permanent leave to remain (2,846,820).

A further 2.3 million (2,327,850) were granted pre-settled status, meaning they need to reapply after living in the country for five years to gain permanent residence.

Of those, an immigration status was granted for 295,890 people from countries like India, Pakistan and Brazil under the scheme, which allows family members who are not EU or European Economic Area nationals to also apply.

The Home Office bulletin said: “Across all nationalities, the highest numbers of applications received were from Polish, Romanian and Italian nationals. This has been the trend throughout the life of the scheme.”

There were 109,430 applications refused, 80,600 withdrawn or void, and 79,730 were deemed invalid, where the Home Office decides someone is not eligible to apply or has failed to provide sufficient proof of residence.

The Home Office said 8% of the applications were from “repeat applicants” (472,220).

Among the applications were more than one million from children (1,002,280).

Some 772,260 of the applications from under-18s finalised by the end of June were granted an immigration status, while 32,870 requests were refused, withdrawn, void or invalid, the figures indicate.

By council area, Newham in east London saw the highest number of applications to the scheme (142,120). Outside London, this was seen in Birmingham in the West Midlands (138,490).

It is still not known how many people in the UK are eligible for the scheme but could remain in the country undocumented.

Anyone who has not yet applied effectively lost their lawful immigration status after the deadline.

Late applications can be made under limited reasonable grounds and the Government has said there is no cut-off date for doing so.

Those who applied before the deadline but have yet to receive a decision will have their existing rights protected, subject to the outcome of the application and any appeal.

Anyone who does not apply and continues to live in the UK without being able to prove their immigration status could face enforcement action.