The Labour leader reportedly told The Guardian that although he opposes the airport's expansion, there is "huge debate in the party about it".
Asked whether he would tell his MPs to vote against expansion, he told the paper: "What I've discovered is whipping Labour when Labour doesn't want to be whipped is not an easy thing to do."
The Telegraph reported earlier in September how Theresa May apparently favours a third runway at Heathrow over a second one at Gatwick.
Heathrow wants 25,000 extra flights a year from 2021
It said the prime minister planned to give her MPs a free vote on the matter, with a number of high-profile Conservative politicians vehemently opposed.
Recent newspaper reports suggest a majority of MPs within both the Labour and Tory ranks would vote in favour of expanding Heathrow, given the chance.
Mr Corbyn's comments came as Heathrow Airport announced on Thursday (September 29) it wants to operate 25,000 extra flights a year from 2021.
It said the additional flights should be allowed in the four years leading up to a third runway opening in 2025, should expansion get the go-ahead.
The airport claimed the extra flights would give the British economy a £1.5bn "Brexit boost" by unlocking the benefits of a third runway early.
'Post Brexit cloak of subterfuge and spin'
But local authorities rounded on the proposal, saying the extra flights would "cause distress to millions of people in west London".
In a joint statement, Richmond , Wandsworth, Hillingdon and the Royal Borough of Windsor and Maidenhead councils accused Heathrow of attempting to dress up the "weaknesses" of its plans in "some post Brexit cloak of subterfuge and spin".
The Airports Commission last year recommended a third runway at Heathrow should be built , increasing annual flights at the airport from 480,000 to 740,000, but only if numerous conditions could be met.