Shadow Brexit Secretary Keir Starmer said the party will not back Independent MP Sarah Wollastons amendment.
The motion states the UKs exit from the EU should be delayed so another public vote can be held.
Starmer said in the House of Commons: "Those pressing this amendment seem to be out of step with the vast majority of co-campaigners campaigning for exactly the same cause.
"They may genuinely have a difference of opinion, but we will not be supporting it tonight."
The Peoples Vote campaign has also objected to the vote being held tonight.
REJECTED: Shadow Brexit Secretary Keir Starmer confirmed it this afternoon (Pic: GETTY)
A spokesperson said: “The Peoples Vote campaign does not instruct its supporters in Parliament on how to vote.
“We recognise there is a range of opinions on when to press the case for the public being given the final say, which means some of these MPs will vote for the Wollaston amendment, some may vote against, and some will abstain.”
Labour will whip its MPs to abstain, the Daily Mirror reports.
Westminster SNP leader Ian Blackford accused Starmers party of being a “fraud” for failing to back another referendum tonight.
He said: "I say to him, our friend and colleague, we have that opportunity with the amendment today to express the views of people in the House of Commons that we must have a People's Vote.
"I implore him not to stand against the amendment today or I'm afraid that Labour will be found out for what they are – a fraud and they are participating in Brexit happening if they fail to back the People's Vote this afternoon."