A Conservative minister sparked alarm among EU nationals after appearing to suggest thousands of people without settled status could be deported after Brexit.

Brandon Lewis, the security minister, said European citizens living in the UK risked being sent home if they fail to apply for permanent residence by the end of 2020.

“If EU citizens have not registered by then without an adequate justification, the immigration rules will apply,” he told the German newspaper Die Welt.

Asked whether people face deportation despite fulfilling all legal conditions for a residence permit, Mr Lewis said: “Theoretically, yes. We will apply the applicable rules.”

Campaigners seized on his comments as a sign that EU citizens will “face the full force of the hostile environment”.

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Mr Lewis later said his remarks were taken out of context and said the government would “allow time” for those with reasonable grounds for missing the deadline.

Theresa May repeatedly promised that the more than 3 million EU citizens in this country have no reason to fear deportation.

The row comes after new Home Office figures revealed more than 2 million EU nationals have asked to remain in the UK, with a spike in applications in September amid fears over a no-deal exit.

Maike Bohn, a spokesperson for EU citizens’ rights group the3million, said: “This is no way to treat people, let alone what was promised.

“We don’t know at all how many people will need to apply – there are no reliable data on the number of EU citizens living in the UK – and there will never be a 100 per cent success rate for a new scheme like the EU settlement scheme.”

Ms Bohn, an EU citizen with a German passport, added: “Those people who miss the tight deadline will face the full force of the hostile environment.”

Yvette Cooper, chair of the Home Affairs Committee, said it was “outrageous” that people with a legal right to be in the UK could face deportation in just 14 months’ time.

She said: “Given the many issues with the operation of the settlement scheme so far, there are bound to be people who do not or cannot apply by the deadline.

“The Home Affairs Committee has been warning the government about this problem for a long time. Instead of these threats, the government should enshrine people’s rights to stay in law so they are protected and not put at risk by failings in a bureaucratic process – as the Home Affairs Committee has recommended.

“It is clear that the government have not learned the lessons from the Windrush scandal, which showed how easily individuals can fall through gaps in the system through no fault of their own, and how easily lives can be destroyed if the government gets this wrong.”

Christine Jardine, the Lib Dem home affairs spokesperson, said it was clear that Boris Johnson had no intention of automatically guaranteeing the rights of EU citizens.

She said: “No one seriously believes the Home Office will have granted settled status to all 3.6 million EU citizens by the Conservatives’ arbitrary December 2020 deadline.

“Thousands will inevitably be left effectively undocumented – and now the government is saying it will deport them. That is totally unacceptable.”

A Home Office spokesperson said: “EU citizens are our friends, family and neighbours and we want them to stay.

“The EU settlement scheme is a free and easy way for EU citizens to get the UK immigration status they need.

“We have received 2 million applications and are looking for reasons to grant status, not refuse, and EU citizens have until at least December 2020 to apply.