She rejected Mr Lewis" claim it was an "honest mistake" made by the whips, describing it as "neither honest nor a mistake'.
Brandon Lewis, the Chairman of the Conservative Party, voted on a key vote on the customs union on Tuesday after being told to break his pair by Mr Smith.
It emerged yesterday Lib Dem leader Sir Vince Cable was at a meeting discussing how to stop Brexit when he and predecessor Tim Farron missed two knife-edge Commons votes on Monday.
Senior Labour MP Harriet Harman is leading current efforts for MPs to be given six months' maternity leave, with provisions for colleagues to vote on their behalf during their absence.
Dawn Butler MP, the shadow minister for women and equality, said: "If these reports are correct, the Tory whips, Brandon Lewis and even the prime minister have been telling untruths about their shocking move against an MP on maternity leave. "That is an order not a request" was how text was retold to me".
A Conservative spokesman stopped short of denying the reports.
'This is calculated, deliberate breaking of trust by whips and chief whip Julian Smith to win at all costs.
"We need a full, honest explanation of what's gone on".
Labour said the Chief Whip and the party chairman should quit if they could not account for what happened.
The Tory MP Heidi Allen said: "I sincerely hope this isn't true". No matter how tough the going gets, principle, integrity and standards matter.
A fellow Conservative Andrew Bridgen cast doubt on claims the episode was an honest mistake.
But according to The Times, Mr Lewis and two other MPs were told by Mr Smith that they should vote, despite being paired.
A statement released by the Conservative party said: "We have apologised for the fact that a pregnancy pairing arrangement was broken in error this week. No other pairs offered on the trade bill on Tuesday were broken".
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.
"It wasn't good enough and will not be repeated".