European citizens who have applied for settled status are being detained and threatened with deportation, a development that contradicts assurances from ministers and appears to contravene the Brexit withdrawal agreement.

The Home Office has served EU nationals with removal directions even though they could prove they had applied for settled status, which should protect their rights to remain in the UK.

Ministers have repeatedly promised that anyone who had applied by the 30 June deadline would have their existing rights protected while their case was heard.

The apparent failure to honour that agreement has prompted accusations of either “administrative incompetence” by Home Office officials or a “wilful” attempt to deport as many EU nationals as possible on the assumption they are easier to remove, for instance, than asylum seekers.

A letter from the legal charity Bail for Immigration Detainees (Bid) to the head of immigration enforcement, dated 29 July, raises concerns over the Home Office’s failure to acknowledge receipt of settled status applications in cases where it wants to deport EU citizens.

Bid says that unless a meaningful response is received from the Home Office by the end of this week, it will make an official complaint to the European Commission.

Lawyers argue it marks an important battle to protect the rights of EU nationals following Brexit. They warn that the failure to acknowledge applications could potentially affect thousands of individuals.

On Friday an EU citizen whom the Home Office wanted to deport, and who had been detained in an immigration removal centre, secured their release on bail after a judge accepted that they could not be removed because they had made an EUSS application.

Even so, the Home Office still contested their release and offered no apology or explanation why it had earlier argued there was no evidence of the application at a previous hearing and therefore could deport them.

Speaking shortly after being released, the EU national, who requested anonymity, told the Observer: “They’re trying to play with mine and my family’s lives and it’s not fair. I’m supposed to have rights.”

Pierre Makhlouf, legal director of Bid, said: “It seems that the Home Office has pre-decided the fate of certain EU nationals, perhaps believing that they are easy to remove. But in its drive to deport more people, it is side-stepping legal requirements and procedures.

“Whether this is due to administrative or wilful neglect may be unclear, but by ignoring the legal steps that EU nationals have undertaken to assert their rights, the UK is in breach of the its duties under the withdrawal agreement.”

The issue appears to relate mostly to applications sent by post instead of forwarded digitally. Araniya Kogulathas, a barrister and legal manager of Bid’s EEA (European Economic Area) project, said paper applications were used by many vulnerable and marginalised people, including the elderly and those in detention or prison who found it difficult to access a computer or didn’t have access to a valid identity document.

The numbers affected could be significant. For instance, out of 1,500 inmates at Wandsworth prison, south London, almost 500 are believed to be EU nationals.

Kogulathas said: “Despite having made EUSS applications, EEA nationals are being deprived of their liberty and even served with removal directions, both of which they are forced to challenge despite limited access to legal advice and representation.

She added: “These challenges are particularly difficult for those detained under immigration powers in prisons, some of whom are locked in their cells for around 23 hours a day or more due to the pandemic.”

Aware of such difficulties ministers have promised an indefinite period where people who had not applied would be allowed to do so, if they had reasonable grounds.

Among the cases known to Bid are one where the Home Office failed to acknowledge an EUSS application submitted in mid-July, stating that there were “no barriers to his removal and removal directions are to be set soon”. Another case involved an EU citizen who, despite submitting an EUSS application online, still received removal directions from the Home Office.

A Home Office spokesperson rejected the claims as “completely baseless” and despite a number of cases featured in the article having been contested by the Home Office in immigration tribunals – the latest of which occurred on Friday – claimed “the Observer had failed to provide any proof whatsoever that detention or removal directions are being served to those with EUSS Settlement Scheme Status”.

They added: “Our approach means that should immigration enforcement encounter anyone without EUSS but who may be eligible, we will work with them to enable them to apply and signpost them to available support. If someone has applied to the EU Settlement Scheme by the 30 June deadline, but has not had a decision yet, their rights are protected until their application is decided.”