Theresa May has said she was surprised that the Commons Speaker, John Bercow, had allowed MPs to vote on Dominic Grieve’s Brexit amendment on Wednesday, and called on him to explain himself before parliament.

The amendment compels the government to say within three sitting days what it will do if, as expected, May’s Brexit deal is voted down next Tuesday – giving her a deadline of Monday 21 January to make a statement on the government’s intentions.

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The prime minister said there should be “consistent interpretation” of the rules as she waded into the row about Bercow’s decision to allow Grieve to submit an amendment on a government motion that was intended not to be altered.

Speaking at a press conference alongside the Japanese prime minister, Shinzō Abe, May said: “Obviously the Speaker made a decision on a particular amendment; I was surprised at that decision.”

She called on Bercow “to explain that decision” and endorsed a call made by Andrea Leadsom, the leader of the Commons, on Wednesday to “publish the advice that he had received” from the parliamentary clerks.

May has no power to dismiss Bercow, who has been in the job for over nine years. His appointment is a matter for the whole House of Commons, and the Speaker retains the support of pro-remain Conservatives as well as opposition MPs.

But she warned that the Speaker was at risk of making up the rules as he went along. “Members of Parliament need to know that there is a set of rules in the House of Commons; they need to know that there will be consistent interpretation of those rules so that they know how they can operate within the House,” May said.

Grieve’s amendment passed on Wednesday by 11 votes after Bercow allowed it to be debated. Government business managers had submitted a procedural motion for the Brexit debate that they said was unamendable, but Bercow directed his clerks that it should be taken for debate.

Earlier, a defiant Bercow had told MPs that “there was nothing arbitrary about the conduct of the chair yesterday” when he was accused of arbitrarily changing the rules by Leadsom in the Commons.

“This Speaker is well aware of how to go about the business of chairing the proceedings of the House because he’s been doing so for nine and a half years,” Bercow said, describing criticism as “water off a duck’s back”.