Chief Whip Julian Smith, the Skipton MP, apologised and said Tory Party chairman Brandon Lewis had been "asked to vote in error" after a pairing agreement with a senior opposition MP on maternity leave was broken.
Tory whips had agreed to "pair" her with party chairman Brandon Lewis - meaning he would also skip the vote so Ms Swinson would not be punished for having a baby.
Jo Swinson, the party's deputy leader, is at home with her two-week-old son Gabriel and was "paired" with Mr Lewis for the critical vote that could have caused a crisis had the Government lost. I think it was an honest mistake made by the whips in fast-moving circumstances.
Tory sources say Mr Smith "might have told" some MPs to break "short term" pairing deals but, if he did, none went through with it.
Furthermore, it's claimed that Smith urged two other Tory MPs that had been paired, to vote on new clause 18 - both sought clarification and ignored his instruction, according to the Times.
The pairing system was implemented to make Commons votes fairer - if an MP is unable to vote, they are paired with an opponent on the other side of the argument who must sit it out.
She continued: "Just how low will your Government stoop Theresa May?"
Image Brandon Lewis said it was an 'honest mistake'
She said it was "absolutely abhorrent to be calling out me in particular" and, referring to the Swinson breach, added: "I assured the house yesterday that it was an error".
A Conservative spokesman stopped short of denying the reports.
The Tory MP Heidi Allen said: "I sincerely hope this isn't true".
Labour has called for the chief whip and party chairman to resign if they can not fully explain what happened. No matter how tough the going gets, principle, integrity and standards matter.
The shadow equalities secretary Dawn Butler said: "We need a full, honest explanation of what's gone on".
Mrs May's spokeswoman insisted she retained full confidence in her Chief Whip.
The chairman of the Conservative Party has apologised after he broke a pact with a Lib Dem MP who had given birth just days before.
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