Rangers claim the "re-refereeing of games" is putting unfair pressure on match officials.
Ibrox managing director Stewart Robertson has called for clubs to seek change from the Scottish Football Association after criticising the approach of compliance officer Clare Whyte, who replaced Tony McGlennan in late August last year.
The complaint comes after Rangers goalkeeper Allan McGregor received a retrospective two-match ban for a studs-up challenge on Aberdeen's Lewis Ferguson.
Robertson told his club's official website: "If you go back to last season and previous seasons, it was only incidents of violent conduct or off-the-ball incidents the referees didn't see that would be reconsidered.
"What we are now getting ourselves into is a situation where many more incidents are being looked at and we are effectively re-refereeing the games.
"That is placing intolerable pressures on the referees, which is then placing pressures on the compliance system and the disciplinary system.
"We feel we should now be looking to go back to what the system was previously where it was violent conduct and off-the-ball incidents that should be reviewed only."
Nine top-flight players have received notices of complaint from the SFA so far this season. Five of the suspensions have been accepted by the clubs involved and the other four were upheld by an independent judicial panel.
Whyte must first receive unanimous approval from three former match officials before issuing a notice of complaint.
The SFA's online disciplinary updates only go back to December 2017 but there were only three notices of complaints issued to Premiership players – all accepted – during the final six months of last season.
Robertson said: "Clare came in at the start of this season and there is no doubt things have been dealt with differently this year.
"Some of the incidents which have been reviewed this year wouldn't have been reviewed last year. That is leading to the confusion – there is much more inconsistency and it definitely feels as if we are re-refereeing games.
"It also feels as though the incidents, which are being highlighted on the television at the weekend, are the incidents which are being picked up by the compliance officer on a Monday."
McGregor is the only Light Blues player to receive a retrospective ban this season, which came following a failed appeal from his club.
Rangers have twice appealed against red cards handed to Alfredo Morelos – once successfully – and failed to overturn a controversial second yellow card for Daniel Candeias on the grounds of mistaken identity.
Robertson called for clubs to "speak with one voice and at least get around the table and debate what should change".
"We have had informal contact from the SFA and we wrote to them last week requesting we have a detailed review of the disciplinary system," he added.
"I am sure they will be in touch informally with us but from the discussions we have had informally, I know there are a lot of other clubs who have similar views on how the system is working at the moment and the inconsistencies which are being created by the way in which the system is being interpreted."
The SFA declined to comment.
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