Boris Johnson has urged EU citizens eligible for settled status in the UK to "get on with" applying, as government advisers warned tens of thousands could miss the deadline.

The Prime Minister said there had already been time extensions, that it was five years since the referendum result, and the Government had funded 72 organisations to help vulnerable EU citizens to apply.

"Anybody applying within the deadline will have their case dealt with and I urge them to get on with it," he told MPs.

His appeal came amid concerns that at least 100,000 EU citizens eligible for settled status will effectively become illegal migrants after the deadline has passed at midnight on June 30.  

Some estimates suggest the number could be as high as 500,000. About 5.6 million EU citizens have so far applied for settled status, two million more than originally anticipated.

Failure to apply could ultimately deny the EU citizens and their families the right to live and work in the UK or to claim benefits, although the Home Office has stressed anybody found by immigration enforcement officers will have a 28-day grace period to submit an application.

The department has said that even then, they will still be allowed to apply after the 28 days provided there are "reasonable grounds". 

The “reasonable grounds” for missing the deadline will include where a parent, guardian or council has failed to apply on behalf of a child, or where a person has a serious medical condition preventing them from applying in time.

Madeleine Sumption, director of Oxford University’s Migration Observatory, and member of the Migration Advisory Committee (MAC), said that even if a “tiny fraction” of the 5.6 million missed the deadline, it could amount to more than 100,000. “There is the potential for it to be pretty big,” she said.

She said the Government was giving those who had reasonable grounds the benefit of the doubt, but there would be “uncertainty in the longer term” as the Government took a stricter approach in time.

“In some cases, it may be some years before someone realises. There are legal complexities if they are trying to get a new job. They would have to get a decision on their status,” she said.

EU migration to the UK fall to zero

There are said to be as many as 70,000 missing applications among the 820,000 EU citizens claiming benefits, equivalent to about 8.5 per cent. That would suggest as many as 500,000 EU citizens could have missed the deadline, if replicated across all EU citizens in the UK.

Jakub Kruba, a Polish community leader in the UK, said there were estimates that between 20,000 and 100,000 Poles eligible for settled status may have missed the deadline, equivalent to up to 10 per cent of the 930,000 Poles that had so far applied.

He said the Government’s marketing campaign had not reached some sections of the Polish community because it had been predominantly in English. Many could speak English for day to day business, but some struggled when dealing with complexity of immigration law, he said.