Hundreds of fans of champions Melbourne Victory and Western Sydney Wanderers, two of the best supported clubs in the league, walked out after half an hour of their matches last weekend.
The protests were triggered by the publication of a list of 198 fans banned from stadiums around the country in Sydney's Sunday Telegraph newspaper.
The leak brought to a head long-running dissatisfaction among supporters groups with Football Federation Australia's (FFA) treatment of fans as well as a perceived lack of due process in the handing out of bans.
Australian football bosses promised to put in place an appeals process for the supporters banned from stadiums but FFA Chief Executive David Gallop defended the league's banning policy on Tuesday, further angering fans groups.
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The Red and Black Bloc, a Western Sydney supporters group, said they would boycott the match against Brisbane Roar on Saturday "in its entirety" and demanded a meeting with the league's bosses.
"This is the only way to continue sending a strong message to the FFA that we will not stand for their inept administration of our game," the group wrote on their Facebook page.
Sydney FC's 'The Cove' supporters' group said they would also boycott the team's home game against Newcastle Jets on Friday.
"We have consulted with numerous other fan groups, most of whom will do the same," the group said on their Facebook page.
The FFA have been criticised by players and media pundits for their policy of issuing universal bans to fans for unruly conduct, even if they are not convicted in the courts.
"At the end of the day it needs to be settled quickly because the game won't survive without the fans and we need them on board," Central Coast defender Justin Rose told Sky Sports Radio on Wednesday.
"I think the fans, it's good that they are uniting together, they need to stick up for what's right."
FFA boss Gallop defended the league's policy but reiterated that fans could have their bans overturned if they produced evidence that they were not involved in anti-social behaviour.
"These are serious offences," he told reporters.
"Many assaults, many ignitions of flares, the throwing of projectiles at coaches and players and invading pitches. These are not trivial matters."
(Reporting by Ian Ransom; Editing by Peter Rutherford)
