With Perth sitting in fourth spot just a point adrift of league leader Wellington, its charge towards a first Premier's Plate - and even a finals appearance - is in jeopardy.
Football Federation Australia (FFA) issued Glory an initial show-cause notice on 12 February with further concerns prompting a second one to be sent late Wednesday.
A-League chief Damien De Bohun on Thursday said investigations revealed serious concerns about the club's compliance with the salary cap and the amount of the alleged breaches placed Glory significantly over the $2.55 million cap.
He said Glory now faces the loss of competition points and/or hefty fines if found guilty.
"We take situations of deliberate concealment much more seriously than simple administrative mistakes and debates around the interpretations of the regulations and the amount of the alleged breaches would place Perth Glory significantly over the salary cap this year," De Bohun said.
"We have now uncovered a range of information that needs to be explained and that's what has led us to sending the second show cause notice yesterday.
"It relates to a number of contracts for a number of players."
While not revealing the amount in question, De Bohun said it involved several things including payments outside of standard player contracts, payments of player agents fees, travel costs and accommodation allowances.
FFA is also investigating payments to a player's family member believed to be related to star striker Andy Keogh, who has been integral to Glory's success this season.
De Bohun said FFA had spoken to numerous people at all levels at the club and that sanctions could be imposed at both a club and individual level.
"We rate the integrity of the competition as the single most important thing in the A-League so we've worked through this with a number of people both with players, administrative staff right through to their board."
Glory has until Wednesday next week to answer the latest matters with De Bohun confident the issue would be resolved before the finals kick off on 1 May.
It now remains to be seen whether Glory is part of that finals picture.
"It's a tremendous race this year to the finals and we want to make sure that every fan out there knows that their club has an equal chance of success," De Bohun said.
Sydney FC was fined $129,000 and docked three points in 2006 in the only other reported case of salary cap breaches in A-League history.
