The Green Brigade fans group has accused Celtic of invoking an "evidently unfair" suspension of its members.
Fans who have registered with Celtic as members of the ultras group have had their season tickets suspended pending a review as well as being denied tickets to away matches.
Celtic cited an "increasingly serious escalation in unacceptable behaviours" for their decision.
There were hundreds of empty spaces at the bottom of the standing section as Celtic kicked off their cinch Premiership contest with St Mirren on Wednesday night.
The mass suspension came after Celtic received two UEFA fines, for a pyrotechnic display at Feyenoord and an anti-fascist banner which contained "offensive" language towards Lazio in Italian.
The club also cited supporters "rushing turnstiles and forcing open fire exits to permit access to individuals without tickets and pitch incursions" at Fir Park, "intimidating and threatening" behaviour towards stewards and staff, plus "unauthorised displays".
Thousands of supporters across Celtic Park defied club appeals as they displayed Palestine flags ahead of the Champions League clash with Atletico Madrid last Wednesday, a move which is likely to lead to UEFA sanctions.
A Green Brigade statement claimed the PLC board had "shamed" the club over attempts to "censor and sanction Palestinian solidarity".
The group added: "It is undeniable that the sanctions imposed against those affiliated with the Green Brigade are a result of the group’s unapologetic solidarity with Palestine.
"The sanctions applied, most notably collective bans, are evidently unfair; bereft of policy, process and communication with individuals wrongfully being punished before receiving any allegation, any evidence nor any right of defence."
They added: "As an ultras group, known for boisterous support and creativity, we occasionally breach the assorted regulations which are in place to sterilise football stadiums.
"Whether it be an anti-fascist banner against Lazio or Palestine flags against Atletico Madrid, we have no regrets in by-passing stadium security checks to produce displays which are clearly welcomed by the Celtic support as well as audiences from much farther afield."
The group "categorically" denied breaking in to the stadium and suggestions of intimidating, threatening and abusive behaviour towards staff.
Celtic issued a statement on Tuesday night explaining their decision.
A club spokesperson said: "To avoid any misunderstanding, the progressive steps taken by the club over a period of time are as a result of an increasingly serious escalation in unacceptable behaviours and non-compliance with applicable regulations, at matches at Celtic Park and away grounds over a period of time, which are creating serious safety concerns and other issues."
