FFA chief executive David Gallop does not believe active supporter groups should have their privileges rescinded over the indiscretions of a minority.
Melbourne Victory are now heading down the same disciplinary path as Western Sydney after being served a show-cause notice on Monday for bringing the game into disrepute.
Their alleged crime is the same as the one that earned the Wanderers a suspended three-point deduction and $50,000 fine last week - troublesome fans who let off flares and commit other unsociable acts during matches.
Seven flares were ripped inside and outside AAMI Park before and during Saturday night's Melbourne derby, sparking further outrage at a time when the game needs it least.
The weekend before at Etihad Stadium, fans seated in the Wanderers' away bay lit around 25 flares and set off detonators at their match with Victory.
It's a pattern with no clear-cut solution, and one that prompted Victoria Police to threaten revoking the coveted privileges reserved for active supporter groups, such as sitting together behind the goals and waving giant flags.
But while FFA maintained their zero-tolerance approach to troublemaking fans on Monday, Gallop was adamant the spectacle should not be ruined for the vast majority who don't condone the behaviour.
"Not necessarily, no," Gallop said on Monday.
"We work to manage the plans that fan groups have almost every week.
"There are different levels of planning.
"For big games, the planning starts some weeks out with authorities, police and venue security, and what is going to be authorised and what isn't is worked out.
"We're not suggesting changes to that."
Gallop said it would be a "great shame" if Victoria Police made good on last week's threat to shut games down if trouble persists, suggesting it would undo the governing body's painstaking work to address the complex issues surrounding fan relations and football's reputation in Australia.
"The police have got the power to do that clearly," he said.
"It would be a catastrophic result.
"All the processes we're putting in place, including these improvements to the fan banning process, are about making sure we're never in that situation."
For Victory's part, chief executive Ian Robson was unforgiving of those whose stupidity left the club scrambling to submit a response they hope will persuade FFA not to impose the same punishment dished out to the Wanderers.
"We cannot say strongly enough how disappointed we are to find ourselves in this situation," Robson said.
"Our resolve (to eliminate flares) only gets hardened as a consequence of the very disappointing circumstances of Saturday night.
"We refuse to allow the reckless behaviour of a small minority define what this club stands for."
While Victory's transgressions were deemed less severe than Western Sydney's, Robson intimating the fact that Victory fans were 'on notice' leading into the match made their actions just as bad.
"These acts of these individuals show they do not care for the club, and they do not care for the code or this league," he added.
Gallop was encouraged by Robson's condemnation.
"We'll look carefully at what they say in their submission, encouraged by what Ian Robson said today and the seriousness with which they're taking the issue," Gallop said.
"But it's appropriate they get an opportunity to state their position before we make a decision."
On Monday the FFA Board discussed the implementation of a flare management system, which is set to involve education programs, prevention and sanctions.
It also ratified the promised new fan-banning procedure, which allows fans accused of bad behaviour to view evidence used against them and appeal to an independent body before they are banned from stadiums.
