The government is warning that a proposed new system to document EU migrants who have arrived in the UK during the Brexit transition period has "barely begun", according to reports.

Theresa May previously announced that any EU citizens who come to the UK post-Brexit will not get the same rights to stay in the country as the three million who are already here.

The prime minister announced this decision despite warnings form the Home Office that a separate system will need to be created to separate existing EU migrants with newly arriving ones.

As well as creating a whole new registering system, at the same time the Home Office will also need to work on implementing a new immigration system – which is still under negotiation.

Government sources are now warning that work creating a new system has barley started and will "almost certainly" not be ready when Britain officially leaves the EU next March, reports the Times.

One government source said: "The way things look at the moment it almost certainly won't be ready. The government doesn't have the best record of these kind of projects anyway and the most pressing priority is to ensure that nothing goes wrong with registering existing EU nationals. If that goes wrong it will be a disaster."

According to reports, the Home Office were working on the assumption that newly arriving EU citizens to Britain will be treated the same as those already here as recently as January.

Jacob Rees-Mogg, Tory MP for North East Somerset, told The Times: "If this were true, it would be a sad admission of incompetence at the Home Office and it would be hard to believe that someone as efficient as Amber Rudd would accept such a sorry state of affairs."

A Home Office spokesperson said: "The prime minister has been clear that during the implementation period there will be a registration system for EU citizens coming to the UK.

"The precise details of the implementation period are currently being negotiated with the EU, but planning is well under way."

Theresa May
Prime minister Theresa May leaves 10 Downing street in London on 7 February Getty