More than 300,000 applications for the EU settlement scheme are waiting to be processed just weeks before the deadline for entries, figures suggest.

EU citizens and their families are asked to apply to the Home Office scheme by the end of June, in order to continue living and working in the UK now the Brexit transition period and freedom of movement has ended.

According to provisional Home Office figures to the end of May, 5.6 million (5,605,800) applications have been received since the scheme opened in March 2019 and 5.2million (5,271,300) have been finalised.

This leaves around 334,500 applications which were yet to be processed at the end of last month, the figures suggest.

The Home Office said it usually takes around five working days for complete applications to be processed, but it can take longer than a month if more information is needed.

The department has not committed to completing all applications before the deadline as, for example, submissions could be made up until minutes before.

Those who apply before the deadline, but have not received a decision by then, “will have their rights protected until their application is decided”, the department said.

Immigration minister Kevin Foster described the scheme as “an extraordinary achievement in securing the rights of EU citizens living in the UK”, adding: “We urge everyone eligible to apply before the June 30 deadline and will continue to leave no stone unturned in helping those who need support.”

There are no plans to extend the deadline, despite calls from campaigners to do so amid the coronavirus pandemic, but from July anyone eligible for the scheme can make a late application where there are “reasonable grounds” for missing the cut-off, the Home Office said.

Questions remain over what will happen to those who stay in the country after the deadline who have not applied so do not have an immigration status under the scheme, or if their application has been refused.

But it is thought rights will also be protected while decisions are appealed.

Maike Bohn, co-founder of campaigner group the3million which seeks to protect the rights of EU citizens living in the UK, described the backlog as “worrying”, adding: “We need these numbers to go down fast, not creep up.

“From 1 July, landlords and employers will be wrestling not just with a new and digital-only immigration status but whether someone has an application pending with the Home Office.

“This information overload is a recipe for disaster. We are already seeing people getting it wrong because of the complexity.”

Of the concluded applications, more than 2.7 million of those (2,754,100) were granted settled status, allowing them permanent leave to remain.

A further 2.2 million (2,276,200) were given pre-settled status, meaning they need to reapply after living in the country for five years to gain permanent residence.

But some people have repeatedly applied, leading to duplicate applications.

As of March, 6% of applications were from repeat applicants (311,870).

This suggests an estimated 4,963,560 people had applied to the scheme up to the end of that month, according to the Home Office.

The latest statistics show 94,000 applications have been refused, 72,100 were withdrawn or void and 74,900 were deemed invalid – where the Home Office decides someone is not eligible to apply or has failed to provide sufficient proof of residence.