Ms Swinson has not been in parliament since giving birth to her second child on June 29. Pairing allows party whips to designate an MP on the opposite side who does not vote, cancelling out the absence.
However, in two knife-edge votes on Tuesday night, Tory chairman Brandon Lewis cast a vote despite whips having agreed that he would pair Ms Swinson.
She expressed outrage on twitter, asking the Prime Minister: “How low will your government go?”
Mr Lewis voted in two Brexit divisions, one which was narrowly lost by the government on maintaining EU medicines regulations, and a crucial vote that defeated an amendment to keep the UK in the customs union by just six votes.
Last night Mr Lewis apologised, replying on twitter: “I’m sorry Jo. I think it was an honest mistake made by the whips in fast-moving circumstances.
“I know how important the pair is to everyone, especially new parents, and I apologise.”
Conservative chief whip Julian Smith also apologised, saying it had been “a mistake”.
But Ms Swinson called the apologies “nonsense”, saying it was a “calculated, deliberate breaking of trust” and pointing out that Mr Lewis had abstained on earlier votes as agreed, only taking part when the government’s survival was on the line.
The Lib Dems and SNP issued calls for the Commons to vote on a binding motion to bring in proxy voting for MPs caring for newborns in the remaining four days before parliament goes on its summer recess.
There is no formal parental leave system for MPs. A report by the cross-party Commons procedure committee has already set out how one could be set up, including proxy voting for parliamentarians who are absent after giving birth or through illness, but no action has been taken yet.