Socceroos coach Ange Postecoglou says Football Federation Australia (FFA) have done the right thing by sticking firm to their hard-line salary cap stance.

Perth Glory were booted out of this season's A-League finals and fined $269,000 after the club finally accepted its guilt over salary cap breaches.

Some critics have called for the salary cap to be scrapped in the wake of the drama.

But Postecoglou says irrespective of plans for the cap, current rules must be enforced to their full extent.

"Whatever rules are in place need to be protected and honoured," Postecoglou said.

"It's not just about the integrity of the competition this year; it's about the integrity of the competition moving forward.

"You just have to ask Western Sydney and Brisbane Roar how hard it is to hold onto players once you have had success.

"Besart Berisha was running around in a Victory shirt on Wednesday night because Brisbane couldn't fit him in the salary cap.

"Whether there is movement down the track (in regards to the salary cap), that's a separate discussion.

"But whatever those rules are now, it's very important that we are vigilant that we make sure everyone is compliant with them."

The Glory were found guilty of exceeding this season's salary cap by more than $400,000.

Perth threatened to take FFA to court in a bid to overturn the heavy punishment, but the club finally accepted its fate on Thursday night.

Earlier that day, Perth chief executive Jason Brewer apologised for his role in the bitter saga and resigned.

Glory will be relegated to seventh spot at the end of the home-and-away season, meaning the seventh-placed Roar will now earn a spot in the six-team finals.

Perth Glory chief executive Jason Brewer resigned over the A-League club's salary cap breaches. ( Getty Images: Paul Kane )

FFA chief executive David Gallop said he felt sorry for Glory coach Kenny Lowe and the club's players.

Postecoglou shared those views, revealing he had even sent Lowe a text on Wednesday night to see how he was holding up.

"The don't teach you these things in coaching courses," Postecoglou said.

"He's going through a tough time but he's done a good job regardless.

"They have to get through this and make sure they build a bigger and stronger club."

AAP