It is never acceptable for MPs to be manhandled or bullied into voting a certain way, the transport secretary has told Sky News.

Anne-Marie Trevelyan said she was “shocked” to hear what happened during a vote last night in parliament where Conservative MPs have been accused of “manhandling” other Tory MPs to make sure they voted with the government.

She said she voted early so was not there when the chaos ensued but told Sky News’ Kay Burley at Breakfast programme: “It is never acceptable for people to be manhandled or bullied into voting.

“We have seen this happen before where whips perhaps over-egg their encouragement to get people to vote in the appropriate way. That is never right.

“The one thing that our parliament is so revered for around the world is that we allow each of us to vote with our conscience and indeed with our government on important matters.”

She added that she has no doubt the Speaker will be investigating what happened and “it is for him to make the final determination”.

There was confusion just moments before voting started on Labour’s opposition day vote to ban fracking after MPs were told it was no longer a “vote of confidence in the government” – which the whips had said it was earlier in the day and told all Tory MPs they had to vote against the motion or face being suspended.

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In the early hours of this morning, Downing Street sent a message to journalists saying a minister had been told “mistakenly” by them to say the vote was not a confidence vote, but they said Tory MPs were “fully aware” the vote was subject to a three line whip – where they can be suspended if they do not vote with the government.

But asked this morning if it was a confidence vote, Ms Trevelyan said: “No, yesterday was an opposition day debate and the Labour Party were trying to use a parliamentary tool to try and hijack the order paper. That is never acceptable.

“So what it was, was a very important vote to ensure that the government did not allow Labour to do that. It’s a tactic that has been used in the past. And previous governments have also always made sure that those votes are not won by the opposition.”

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She added that those MPs who defied the whip will have discussions with the chief whips, but said there are often “specific constituency reasons or health reasons” for not voting with the government.

Labour MP Chris Bryant took a photo of a huddle of Tory MPs in the lobby looking confused.

He told Sky News: “There was a lot of shouting, there was a lot of speculating, pointing at people, jabbing at people, standing up to whips, squaring up to people.

“And then in a moment, maybe one or two MPs were effectively sort of frog marched through into the division lobby.

“It’s perfectly legitimate for the whips to try and persuade their members by force of reason to vote with them. But it’s not on to intimidate and bully.”

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