Joint A-League leaders Western Sydney Wanderers were Thursday slapped with a suspended three-point penalty and fined Aus$50,000 (US$36,000) after their fans let off a series of flares at a weekend game.

Football Federation Australia punished the club for bringing the game into disrepute through the "dangerous and threatening" behaviour of a section of supporters.

The governing body said an investigation had found fans took part in a pre-meditated and coordinated series of incidents including lighting flares and displaying unauthorised banners during the match against Melbourne Victory.

"The events of last Saturday night and the coordinated misconduct of a section of Western Sydney Wanderers fans cannot be tolerated by anyone in Australian football," FFA chief executive David Gallop said in a statement.

"The misconduct was not only dangerous and threatening but the coordinated and calculated way the fans behaved was a serious blight on the reputation of football and everyone involved in our game including clubs, members, fans, players and officials.

"The sanctions have been set taking into consideration the seriousness of the incidents but a clear commitment both publicly and through its submission that the Wanderers will take responsibility for implementing a clear strategy to identify and exclude these individuals."

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.

The suspended three-point penalty will come into force if any other serious incidents occur in or around any matches the club plays over the next 12 months.

The FFA did not specify what was regarded as a "serious incident".

"The use of flares and associated devices at sporting events are extremely dangerous, illegal and have no place in Australian football," Gallop said.

"We are putting a line in the sand. If these people are true football fans they will understand and appreciate their actions will hurt the clubs they claim to support."

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.