An estimated 900,000 EU citizens in the UK have yet to apply for settled status, which most will need to remain in the country long-term after Brexit.

The data comes a day after the European parliament raised concerns that EU citizens risked discrimination after Brexit in seeking housing and employment.

Home Office statistics for December show that just over 2.7 million EU citizens and their family members have applied for settled status, a special immigration category set up for nationals from member states.

The figures underline a huge take-up of the scheme, which was launched nationally in March 2019, but also show the scale of the task that still lies ahead for the Home Office.

Although there is no official data on how many EU citizens live in the UK, it is estimated to be between 3 million and 3.6 million.

The Liberal Democrats said the figures raised concerns as they showed “more than 1 million EU citizens have now been given the weaker pre-settled status” which is allocated to those who have been in the UK less than five years.

Lawyers have raised concerns that the Home Office may be issuing pre-settled status by default to some citizens who do not, at first glance, seem to qualify for settled status. They have urged EU citizens not to accept pre-settled status, under which they can reapply for settled status, if they have been in the country for longer than five years.

The Lib Dem home affairs spokeswoman, Christine Jardine, said: “Boris Johnson promised to automatically guarantee their rights in law, but today’s figures show that his government’s settled status scheme is anything but automatic.

“Unless the government changes course, tens of thousands of EU citizens will be left without legal rights in less than 18 months – at risk of eviction, detention and deportation.”

Nicolas Hatton, the co-founder of the 3million campaign group, said: “It’s infuriating to see Brandon Lewis gloating about the number of applicants, while refusing to address the main issue of vulnerable EU citizens facing the full force of the law if they do not manage to apply successfully by the June 2021 deadline.”

Lewis, the security minister, said he was pleased with the response to the scheme and urged EU members to put the same effort into guaranteeing the status of British nationals living in their countries beyond Brexit.

He said of EU citizens in the UK: “The UK is their home and the EU settlement scheme has already granted status to 2.5 million people so they can stay.

“We have done more than other EU member states to support EU citizens and it’s time other countries made the same generous offer to the million UK nationals who live among them.”

EU nationals have until June next year to apply to the Home Office for settled status (SS).

According to the data, just over 300,000 of the 2,756,100 people who applied for settled status, are still waiting for a conclusion from the Home Office.

EU nationals have until June next year to apply to the Home Office.

So far, 58% of applicants were granted settled status and 41% were granted the more precarious pre-settled status, which allows people to stay in the UK for a further five years. The Home Office said six applications were refused on suitability grounds.

EU fears over the future of its citizens in the UK after Brexit have mounted since Lewis told a German newspaper last October that EU nationals risked being deported if they failed to apply for settled status.