Scottish Government Brexit Minister Mike Russell said Mrs May's administration in Westminster had "no mandate" to "undermine the devolution settlement".
United Kingdom government sources made clear that the prime minister would not be deflected from her course.
With the Greens, Scottish Labour and the Liberal Democrats having said they will join the SNP and vote against granting consent, it is certain to be passed when MSPs vote on the matter at 5pm on Tuesday.
Scottish Labour, which has been pressing for cross party talks in a bid to end the row, said it was "welcome" both the United Kingdom and Scottish governments had agreed to these.
If UK Prime Minister Theresa May continues to insist on the necessity to pass the withdrawal bill in its current form, it will become the first time in history when the British government adopts a law against the will of Scotland, which may deepen the rift between them.
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But Scottish Labour's Brexit spokesman Neil Findlay said: "As the party that delivered devolution, Labour will always seek to defend and strengthen it".
The UK government and Scottish Tories have so far refused to offer any further concessions after the Welsh government dropped its opposition to the bill and accepted the power-sharing plans on offer.
The UK Government has balked at this on around 24 of the powers being repatriated from Brussels, unwilling to give MSPs an effective veto.
Speaking in Holyrood, he said: "While the UK Government is delivering additional devolution".
"There is a clear solution which is, as I have said and as the committee agreed last week, to simply remove [clause 15] from the bill".
Months of negotiations has seen some agreement, and the Scottish Government are happy with the idea of common frameworks, but as long as Holyrood has the ability to accept or reject them.
"There will be different opinions as to whether we should do that now or in five years or ten years time, but with that body of opinion, a constitutional option like independence is not going to be off the table", she said. "There is a real risk of a no deal Brexit and that would be pretty catastrophic".
He hit out at Labour and the Liberal Democrats for voting with the SNP, and added: "It's patently obvious that Nicola Sturgeon wants a political crisis to provide cover for her independence drive".