MPs in electorates that would be affected by the airport were blind-sided when Mr Shorten called for the airport to be built on the same day as state Opposition Leader John Robertson supported it.
Mr Shorten said Labor believed Sydney needed a second airport and described Badgerys Creek as a "live option".
But while Mr Robertson secured the backing of his shadow cabinet, Mr Shorten did not consult members of the NSW Right in western Sydney, the biggest geographical faction in the federal ALP ranks.
He has agreed to sit down with the group in Canberra on Monday, in what is likely to be the most heated grilling he has faced from caucus members since taking over the leadership.
Ed Husic (Chifley), Michelle Rowland (Greenway), Chris Hayes (Fowler) and shadow treasurer Chris Bowen (McMahon) will all speak against Badgerys Creek and Mr Shorten's support for it.
Anthony Albanese and Tony Burke - supporters of Badgerys Creek - and Jason Clare, who is undecided, will also attend.
But MPs fear the meeting, the first show of disunity against Mr Shorten, will be derailed after details were leaked to Fairfax Media.
"You only leak details of that meeting if you don't want that meeting to go ahead," a Labor source said.
Badgerys Creek has been a political hot potato for three decades and MPs on both sides fear an electoral backlash if it goes ahead.
Prime Minister Tony Abbott has delayed bringing the matter to cabinet amid opposition by Liberal MPs like Fiona Scott who took the bellwether Penrith seat of Lindsay from Labor at the last election.
Labor MPs opposed to Badgerys Creek believe Lindsay and Macquarie, on the slopes of the Blue Mountains, will return to the ALP if the Coalition goes ahead with the airport.
Mr Albanese, whose seat of Grayndler is the most affected by the noise of Sydney Airport, has long backed the development of a second airport.
Last week, he followed Mr Shorten's stance by called for bipartisanship to get an airport at Badgerys Creek built.