Home Office concerns were overruled by the Prime Minister who insisted EU migrants coming to the UK during any withdrawal transition period would not be granted the automatic right to remain, according to reports.
Theresa May's move went against warnings that it would be a struggle to create separate systems to register EU citizens already in Britain and new arrivals, The Times said.
The status of EU migrants arriving in the UK during the proposed transition period between March 2019 and December 2020 has become a flashpoint issue between London and Brussels in recent weeks.
Facing pressure from hardline Brexiteers, Mrs May has insisted that transition migrants could not expect the same treatment as the estimated 3.2 million EU nationals already resident in the UK, while Brussels has said all should be seen as equals.
The Number 10 stance has caused concern in the Home Office, with Government sources saying work on a separate registration scheme had "barely begun" and "almost certainly" would not be ready in time, according to the newspaper.
Downing Street and the Home Office declined to comment directly on the claims.
A Home Office spokeswoman 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."
The claims came as it emerged Billionaire investor George Soros is to pump a further £100,000 into the anti-Brexit campaign.
The move comes after Mr Soros drew fire from Brexiteers when it was revealed he was donating £400,000 to the campaign group Best for Britain to try to halt withdrawal from the EU.
The group revealed Mr Soros's OFS Foundation has also pledged to match crowd-funding to it of up to £100,000.
Best for Britain chief executive Eloise Todd said Brexit could still be stopped by a meaningful vote in Parliament.
"The UK's future with the EU is not a done deal, there is still a vote to come and people across the country deserve to know the truth about the options on the table: one of which is staying and leading in the EU."
Hungarian-born Mr Soros, one of the world's richest men who made a billion dollars betting against sterling on Black Wednesday in 1992, accused critics of a maligning him, telling The Guardian: "I am happy to take the fight to those who have tried to use a smear campaign, not arguments, to prop up their failing case."
The move followed Justice Secretary David Gauke insisting there is no "plot to gag" Cabinet members who want a softer Brexit.
The remarks came after it emerged the three leading Cabinet Brexiteers will all give keynote speeches on the UK's EU withdrawal stance, but Chancellor Philip Hammond will not take part in the co-ordinated bid to set out the Government's position.
Mr Gauke told ITV's Peston on Sunday: "He is not part of the set of speeches that have been outlined today, but that doesn't mean that the Chancellor is not expressing his views both internally in the Cabinet conversations, but also externally.
"So, I don't think that there really is anything in this, that this is somehow any kind of plot to gag a particular faction of ministers. I don't think that's a fair characterisation at all."
Foreign Secretary Boris Johnson will kick-off the Brexit blitz on Wednesday, Valentine's Day, with a call for unity over Brexit.
Mrs May will deliver a major speech on post-Brexit UK-EU security in Germany next Saturday, and will round off the process in about three weeks' time with a keynote address on the overall relationship, following a special "away day" summit of the Cabinet withdrawal committee at Chequers.
Brexit Secretary David Davis and International Trade Secretary Liam Fox will also set out their agendas, but the only minister who backed the Remain campaign in the referendum involved in the process is Cabinet Office Minister David Lidington.