More than six million people applied to Britain's settlement scheme for European Union nationals before its June 30 deadline, including a surge of more than 400,000 in the last month.
After completing its exit from the EU late last year, Britain has started bringing in a new immigration system.
EU citizens who can prove they were living in Britain before December 31 last year will retain the right to work, study and access benefits.
Data showed 6.02 million applications had been received by June 30, of which 5.45 million had been concluded.
"I am delighted that we have secured the rights of so many EU citizens - our friends, neighbours and family members," interior minister Priti Patel said.
Of those concluded applications, four per cent have either been refused, withdrawn or were invalid.
The rest were either accepted as settled or 'pre-settled', meaning residency rights were retained.
A high-profile publicity campaign to remind people to apply reflected concerns some eligible residents may have been unaware of the scheme, or lacked the ability to submit an application.
The number of those who failed to apply in time is uncertain, as are full details of how the government will handle their cases.
Citizens will be given a formal 28-day notice if they failed to apply for settled status, after which they will not be eligible for work or benefits, and will lose the right to services such as free non-urgent healthcare.
The government has repeatedly said it will look to grant status, rather than look for reasons to refuse it to EU citizens, and added the 28-day notice should not be seen as a point when individuals are liable to be removed from Britain.