European Union citizens living in the UK will be deported after Brexit if they have not applied for settled status in time, Home Office Minister Brandon Lewis affirmed on Thursday.

EU citizens in the UK have until the end of 2020 to register for settled status — which will grant them the same rights they currently enjoy — in the event Britain crashed out of the bloc without a deal. If an agreement is found, they will have until June 30, 2021.

"If EU citizens have not registered by then and are not adequately justified, the applicable immigration rules will apply," Lewis told German newspaper Die Welt.

As such, he added, they will be "liable to prosecution for illegal residence and subject to enforcement, detention and deportation measures."

An estimated 3.6 million EU citizens reside in the UK, according to the latest figures from the Office for National Statistics (ONS).

As of August 31 2019, more than 1.3 million EU citizens and their families had applied to the Settlement Scheme, British government figures show.

Read more: What is the EU settlement scheme in the UK and how does it work?

Campaign group The3Million criticised the Home office minister's comments, saying "this is no way to treat people".

"It is not too late to stop this madness of turning law-abiding citizens into unlawful residents," it also said, calling on the government to automatically grant settled status to EU citizens living in the UK automatically instead of having them apply for it.

Stuart McDonald, the immigration spokesperson for the Scottish National Party also backed the automatic grant of permanent residence to EU citizens.

"Finally, a Home Office minister publicly confirms the outrageous implications of the settled status scheme," he wrote on Twitter, adding: "Inevitably, 100s of thousands will end up in this position."

Shadow Home Secretary Diane Abbott from the main opposition Labour party said that "threats by ministers that EU nationals could be deported are a complete breach of all the assurances that the government has made."

"This will be deeply troubling to people who have come here in good faith and who contribute so much to our society," she added in a statement.

Responding to the criticism, Lewis wrote on Twitter that his "words are somewhat taken out of context."

"EU citizens have until at least Dec(ember) 2020 and there's plenty of help available to apply," he added.

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