Conservatives have reacted with anger at the decision by Commons Speaker John Bercow to allow MPs to vote on getting a bigger say on Brexit.
The MPs claim Mr Bercow broke Commons rules and ignored the advice of his own clerks.
The row erupted ahead of five days of debate on Theresa May’s Brexit deal.
Mr Bercow said he had made an « honest judgement » after consulting his clerks « and if people want to vote against the amendment they can ».
MPs, including Commons leader Andrea Leadsom, challenged his ruling in a series of points of order after Prime Minister’s Questions.
They argued that the business motion, tabled by the government, was not amendable and said the Speaker was breaking with historic precedent.
Mr Bercow, who said he was standing up for MPs and Parliament, said MPs would not be able to debate the rebel Tory amendment but would be able to vote on it.
He said had made his decision after speaking to his clerks but rejected calls from Andrea Leadsom to publish the advice he had received.
The clashes in the Commons came ahead of Theresa May launching a fresh push to convince MPs to back her Brexit deal at the start of five days of debate.
The prime minister cancelled a vote on her deal last month at the last minute to avoid a humiliating defeat.
She is hoping new proposals on Northern Ireland will change enough MPs’ minds to save the deal.
But the DUP have already rejected the plans – and rebel Tories are planning a move that could give MPs more say over what happens if her deal is rejected.
The MPs, headed by former Tory ministers Oliver Letwin and Dominic Grieve, helped inflict a defeat on the government on Tuesday on an amendment aimed at making it more difficult to leave the EU without a deal.
Labour has, meanwhile, said it will table a motion of no confidence in the government if Mrs May’s deal is voted down next week.
This whole process is on a deadline. Those who like to think of themselves as moderate are now feeling very radical about forcing the timetable, should the expected happen and the prime minister’s plan be rejected by MPs next Tuesday.
As things stand, if the government hasn’t been able to get its deal agreed in Parliament, they have a couple of weeks to come back and reveal their plan B – the one that Mrs May has been unwilling to share (not surprising when Cabinet leaks like a sieve) and the one that some of her colleagues fear she doesn’t actually have.
There are moves afoot in the form of an amendment today that would force the government to come back with their alternative plan much more quickly – within three days of the likely defeat next week.
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Ahead of the debate ministers have published plans to give the Northern Ireland assembly in Stormont the power to vote against new EU rules if the border backstop comes into force after Brexit.
Mrs May is hoping that giving a greater role to the devolved government, which is currently suspended, will help her win the support of the Democratic Unionist Party for her Brexit deal.
But the DUP’s Brexit spokesman Sammy Wilson said the proposals were « meaningless » and had « no real significance ».
Mrs May’s de facto second-in-command David Lidington said he « would have been surprised had this document of itself been sufficient to shift their position ».
But he said the government would be coming forward with further proposals in the run-up to next week’s vote.
Speaking at Prime Minister’s Questions, Mrs May said MPs would get a vote on whether to extend the Brexit transition period or trigger the backstop if no trade deal is concluded by the end of 2020.
Brexit Secretary Stephen Barclay will spell out further details of the vote in his speech later on Wednesday at the start of the five-day debate on her plans.
Mrs May said the « undertakings and assurances we looking for from the EU » would be made available to MPs before the final vote next Tuesday.
Labour leader Jeremy Corbyn accused the PM of « begging » EU leaders for additional « warm words » on her deal but « not one single dot or comma has changed ».
He asked whether she would call a general election if her deal fails to win MPs’ support next week, « as I hope and expect it will », to give the public a « real say » on what happens next.
Mrs May said she will not, calling her agreement a « good deal » and urging Mr Corbyn to back it.
Environment Secretary Michael Gove said he was « confident » Mrs May’s Brexit deal would pass the vote, arguing that the only alternatives were a no-deal Brexit which would cause economic damage or « no Brexit ».
The UK Parliament passed legislation last year stating that the UK would leave the European Union on 29 March – two years after negotiations on its exit began.
As things stand, the UK will leave without a deal if Mrs May’s deal is rejected.
Brexiteer Conservatives argue that this would be better than Mrs May’s deal, but a cross-party group of MPs are attempting to use Parliamentary tactics to prevent it.
On the eve of Wednesday’s debate, the government suffered an embarrassing defeat when 20 Tory MPs joined forces with Labour to signal their opposition to a no-deal Brexit.
A host of former ministers, including Michael Fallon, Justine Greening and Sir Oliver Letwin, voted to amend the finance bill to restrict the ability of the Treasury to make tax changes in the event of a no deal – and threatened to target other legislation in the coming months.
The same alliance of cross-party MPs will later seek to push through an amendment that would oblige Mrs May to return to the Commons within three days with a fresh plan.
It would also enable MPs to table their own alternatives to Mrs May’s plan, which could include another referendum or measures to prevent a no-deal Brexit.
If MPs approve the amendment to the business motion, the debate on the terms of the UK’s withdrawal and future relations with the EU will continue on Thursday, Friday and Monday before concluding on Tuesday, when Mrs May is expected to address MPs before the vote.
The BBC’s assistant political editor Norman Smith said ministers were under no illusion about the scale of opposition they face – but hoped to gradually chip away at the numbers ranged against them with a series of reassurances over the Northern Ireland backstop.
Further measures are expected to guarantee access to British markets and minimise any divergence between Northern Ireland and the rest of the UK.
The DUP and many Tory MPs object to the backstop, a contingency plan agreed by the UK in December 2017 which the EU has said is necessary in case the two sides do not agree their future relationship or another solution by the end of 2020.
They want the backstop to be removed entirely or a legal guarantee that the UK will be able to leave it unilaterally at a time of its choosing.