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She said it was "frustrating" the two sides could not agree how to guarantee no hard border in Northern Ireland.
The issue could not "derail" the chances of striking a deal, she said.
And she sought to reassure critics of her approach that the UK would not end up in "permanent limbo" tied to EU customs rules.
Meanwhile, ahead of a crunch summit of European leaders this week, German Chancellor Angela Merkel warned a deal was looking "more difficult" because of the border question.
"If it doesn't work out this week, we must continue negotiating, that is clear - but time is pressing," she added.
And Donald Tusk, the president of the European Council, urged both sides not to give up, suggesting a deal "always seems impossible until it is done".
In the Commons, Mrs May faced pressure from both sides of the Brexit debate as she gave a statement to MPs.
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