Western Sydney face the prospect of starting next A-League season in arrears if a Football Federation Australia investigation triggers their suspended points deduction.

Adding salt to their wounds after losing Sunday's A-League grand final 3-1 to Adelaide United, FFA chief executive David Gallop confirmed on Monday that the governing body would investigate the lighting of two flares during the match.

One device was let off in the Wanderers' active supporter bays at Adelaide Oval just before kick-off, and another late in the match.

"It's certainly something we need to look at because we've said very clearly over the last few months that flares are not on," Gallop said in Canberra on Monday.


"It is something in the wash-up today and over the next few days we do need to have a look at."

Adelaide United supporter group Red Army are also alleged to have lit flares on their walk to the stadium.

Fervent Wanderers fan group Red and Black Bloc were chided and coaxed into better behaviour after their club was handed a suspended three-point penalty and $50,000 fine after FFA found Western Sydney guilty of bringing the game into disrepute in February.

The punishment came after a small group of away fans ignited about 20 flares, as well as crowd-frightening detonators, during a match against Melbourne Victory at Etihad Stadium.

A week later, Victory were given the same punishment after poor behaviour at the Melbourne derby, when two flares were ripped, missiles were thrown onto the pitch and a TV news crew outside AAMI Park was allegedly assaulted.

At the time, FFA said similar incidents would trigger the suspended sanction and see a points deduction.A decision by head office is not expected imminently.

"The behaviour of the overwhelming majority of fans was exceptionally good. The fans were passionate, spirited and vocal, but showed respect for each other at all times," an FFA spokesperson said on Monday."

A number of flares were ignited before and during the match, involving supporters of both competing clubs, and some seats were damaged in the venue.

"FFA will conduct a review of the event and will consider full reports."

The Wanderers returned to Sydney today and will cooperate fully with the FFA investigation.

A loss of points would be a painful blow to Western Sydney, still coming to grips with losing the grand final three times in four years.

"We said a long time ago that we don't like that in our game and we want it stamped out," Wanderers striker Brendon Santalab said.

"It's unfortunate it happened, it's out of our players' control and the club's control.

"It's again a minority and we hope that stops."