Conservative deputy chief whip Craig Whittaker warned his MPs that Wednesday afternoon’s vote is a “100% hard” three-line whip.
Ms Truss sought to reassure MPs with concerns that there would be a “robust” process to ensure that local communities consented before fracking went ahead.
The dozens of Conservatives who oppose fracking face being kicked out of the parliamentary party if they do not back the Government’s controversial end to the moratorium in England.
Though unlikely, if the Prime Minister loses the vote now, it is being seen as a confidence motion and she would either be expected to resign or request that the King dissolves Parliament, triggering a general election.
Labour sources said the Tories had walked into their trap and are preparing online adverts to target every MP who backs giving the controversial shale gas extraction the go ahead.
If passed, the opposition day debate motion would guarantee Commons time for a Bill banning fracking once and for all.
Mr Whittaker wrote to Tory MPs, saying: “This is not a motion on fracking. *This is a confidence motion in the Government.*
“We cannot, under any circumstances, let the Labour Party take control of the order paper and put through their own legislation and whatever other bits of legislation they desire.
“We are voting NO and I reiterate, this is a hard 3 line whip with all slips withdrawn.”
The Government amendment supporting giving fracking the go-ahead in areas where local consent is deemed to have been given was also made a three-line whip.
“I know this is difficult for some colleagues, but we simply cannot allow this,” Mr Whittaker wrote.
Mark Menzies, Tory MP for Fylde in Lancashire, where fracking could take place, demanded guarantees communities will be given the “final say”.
He asked Ms Truss to “assure me that local consent will be measured independently and transparently” with no direct involvement for fracking companies in assessing whether there is community support.
The Prime Minister told him: “We will consult on a robust system of local consent, give clear advice on seismic limits and safety before any fracking takes place.”
The consultation will consider “all of the relevant people – the regional mayors, the local authorities and parishes as well as the concerns of those directly affected”.
Tory MP Steve Double, who represents the Cornwall constituency of St Austell and Newquay, argued Labour has “overplayed their hand on this occasion”.
“Whatever your views for or against fracking, Conservative MPs shouldn’t be voting to allow the Labour Party to take over the order paper,” he told BBC News.
But shadow Commons leader Thangam Debbonaire said: “The consequence of making this a confidence vote is that if the Government loses the motion on fracking, the Prime Minister will resign and the government will fall.
“The Tories must urgently confirm this is the case.”
The Prime Minister’s lifting of a fracking ban imposed in 2019 over earthquake concerns breaks a Tory manifesto pledge not to end the moratorium without science “categorically” showing it is safe.
Against the backdrop of the war in Ukraine, Ms Truss has argued that the move is needed to end energy dependence on Vladimir Putin’s Russia.
But Tory MPs in areas where fracking could occur have reacted angrily, and fear the go-ahead could make their re-election even harder amid dire polling for the party.
The moratorium was imposed on fracking, which uses high-pressure liquid to release gas from shale formations, after a series of earthquakes at the UK’s only shale wells at Preston New Road, Lancashire, in 2019.
There are potential shale reserves across northern England, but fracking firms could also seek to drill in southern areas where gas might be found.