It leaves Ms May with just days to convince EU leaders that a hard border - with customs checks and posts – can be avoided, in order to move the talks on to future trade.
But, she told MPs: “To those Labour members who shout how – that’s the whole point of the second phase of the negotiations.
“Because we will deliver this – we aim to deliver this – as part of our overall trade deal between the United Kingdom and the European Union
“And we can only talk about that when we get into phase two.”
The comments are likely to alarm the Irish Government, which believes it has full Brussels backing in demanding an immediate - written – guarantee there will be no hard border.
They came as Ms May finally held her delayed telephone call with Arlene Foster, the DUP leader, but Ms Foster is not expected to travel to London for face-to-face talks.
DUP sources suggested an agreement was still a long way off, while Ms Foster told the Belfast Telegraph she wanted to be “at the table” when the Brexit talks discuss Northern Ireland.
In the Commons, Jeremy Corbyn, said the “shambles” showed the Government was failing, adding: “If they can't negotiate a good deal, wouldn't it be better if they just got out of the way?”
But the strongest pressure on the Prime Minister came from hard Brexit-supporting Tory MPs, who fear she is poised to weaken her negotiating position.
They suspect “regulatory alignment” with the EU – for the entire UK, David Davis said – will curtail the freedom to pursue new trade deals after Brexit, with different rules.
Jacob Rees-Mogg, a leading Tory hard Brexiteer, challenged Ms May to apply a “new coat of paint to her red lines” – warning they were “beginning to look a little bit pink”.
And a second, Pete Bone, fired a warning shot, asking the Prime Minister: “If we have a problem, would it help of I came over to Brussels to help sort it out.”
Ms May’s insistence that the Irish border issue will not be settled until phase two is likely to increase Brexiteer suspicions of close trading alignment for the whole of the UK.
Equally, Dublin is likely to be more concerned about the value of the assurances it will be given in Brussels later in the week.
However, Ms May put in a strong performance, given the pressure she is under, repeatedly telling Tory MPs “nothing is agreed until everything is agreed.
And she hit back at Labour divisions over Brexit, telling Mr Corbyn: “The only hard border around is right down the middle of the Labour Party.”