Commons speaker John Bercow has indicated he will rule on whether Theresa May is allowed to repeatedly make MPs vote on her Brexit deal after it was twice defeated.

On Wednesday Mr Bercow said “a ruling would be made” on the matter with parliamentary convention barring a government from bringing the same motion back to the house over and again.

His comments set him on course for another clash with Ms May’s administration, with government advisors believing they could “disapply” any ruling he makes if they win a commons vote on it.

It comes after cabinet ministers and Ms May’s aides suggested she will bring the withdrawal agreement she negotiated with Brussels back to the house for a third time after it was defeated by 149 votes on Tuesday.

Mr Bercow made his comments after he was questioned about the matter by Labour MP Angela Eagle, who said it would be “out of order” for the government to bring the deal back for a third vote.

The Speaker said: “There are historical precedents for the way such matters are regarded. I don’t need to treat of them now and no ruling is required now.

“There may be people who have an opinion about it, I’m not really preoccupied with that, but a ruling would be made at the appropriate time, and I’m grateful for [Ms Eagle] for reminding me that such a ruling might at some point in the future be required.”

Mr Bercow has sought to build a reputation as a champion of backbenchers against the government and has sided with the commons in most disputes.

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In the past, he has even gone against the advice of expert commons clerks, using his authority to overrule them and allow a government motion to be amended by backbenchers – something which ultimately gave MPs more control of the Brexit process.

On repeat votes, the handbook for parliamentary procedure Erskine May says: “A motion or an amendment which is the same, in substance, as a question which has been decided during a session may not be brought forward again during that same session.”

It says a decision on whether “verbal alterations” amount to real changes are “a matter for the judgment of the chair [in this case Mr Bercow]”.

Government ministers are aware of the potential stumbling block to Ms May staging a third vote on her deal, but believe they have a right to try and “disapply” any disadvantageous ruling – though it would require them to win a vote on it in the commons.

Ms May lost the first meaningful vote on her Brexit deal by 230 votes, and then again by a smaller but nonetheless historically large margin on Tuesday night.

House speaker John Bercow makes unusual noise in House of Commons

Asked after the most recent defeat whether the government would consider bringing back Ms May’s deal for a further vote, the prime minister’s spokesman indicated it was possible.

Cabinet minister Alun Cairns went further saying that the second defeat for Ms May’s negotiated settlement was not “the end of the deal” and that there was still “everything to play for”.