'I'm angry to be treated as second-class citizen'
EU citizens use Windrush scheme to stay in UK
The Home Office says it does not have a figure for the number of EU citizens currently living in the UK, but estimates by the Migration Observatory put it at 3.3 million, excluding Irish citizens who have the right to settled status already.
Mr Lewis told Die Welt (in German): "If EU citizens until this point of time have not registered and have no adequate reason for it, then the valid immigration rules will be applied."
When pressed on whether that would include those who met the legal requirements for residence but did not apply in the next 14 months, he replied: "Theoretically yes.
She said this was the "grim reality" of the government's position, "no matter how many times they repeat the phrase 'EU citizens and their families are our friends, neighbours and colleagues and we want them to stay'".
Those applying for settled status must prove their identity, show they live in the UK and declare any criminal convictions.
Once granted settled status, they can use the NHS, study and access public funds and benefits, as well as travel in and out of the country.
The total number of settlement applications finalised by the end of September was 1.5 million, according to figures released this week by the Home Office.
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. The conclusion in 0.5% of cases was classed as having "other outcomes".
Lib Deb shadow home secretary Christine Jardine said she was "absolutely appalled" by Brandon Lewis's deportation threat and she predicted "thousands" of people would be left undocumented by the "arbitrary" deadline.
She warned it could create another Windrush-style scandal - when individuals who arrived from Commonwealth countries between 1948 and 1971 were wrongly told they were in the UK illegally, despite living in the country for decades.
"Brandon Lewis has finally confirmed what we've known all along: Boris Johnson has no intention of keeping his promise to automatically guarantee the rights of EU citizens living in the UK," said Ms Jardine.