Football Federation Australia on Monday demanded answers from A-League leaders Western Sydney Wanderers over the behaviour of some of their fans, who let off a series of flares at a weekend game.

The FFA has given the club until late Wednesday to argue why they should not be sanctioned for bringing the game into disrepute through the conduct of its supporters.

The governing body said sanctions may include financial penalties and the loss of competition points under the FFA Code of Conduct.

The Wanderers, who won the AFC Champions League in 2014, are joint A-League leaders with Brisbane Roar, six points ahead of three other title rivals.

A "show cause" notice was sent after FFA received detailed reports from Victoria Police, Melbourne's Etihad Stadium management and FFA's security advisers, outlining incidents during the match against Melbourne Victory on Saturday.

Police said up to 19 flares were set off inside the ground and another six outside during the match which ended in a 1-1 draw between the A-League's two biggest-supported clubs.

FFA chief executive David Gallop said he was disappointed in the fans' behaviour.

"FFA has received detailed reports from all stakeholders and has asked the Western Sydney Wanderers to show cause why they should not face sanctions for the behaviour of a group of fans on Saturday night," Gallop said in a statement.

"This behaviour has clearly alarmed many people inside and outside the game. It simply cannot be tolerated."

He added that it was frustrating that it happened at a time when the sport was working hard to rid the game of this type of incident, which tainted all fans.

"That is an unfortunate but very real consequence of this behaviour and it underlines the damage that these troublemakers cause," he said.

FFA said it would also continue to work with police and stadium security to identify individuals and ensure they were subject to the banning procedures.