It is understood the FFA will allege the Glory deliberately exceeded the A-League salary cap limit by approximately $150,000 by paying a player through a third party for the entire season. The fresh accusations could derail the club's hopes of playing in the finals series, with Perth facing the prospect of heavy fines and a possible points deduction should they be found guilty of systematically cheating the cap.

Sources close to the investigation suggest at least $150,000 of star striker Andy Keogh's salary was paid into a bank account held by a family member, listing the transactions as payments relating to a Perth fashion festival. Although Keogh is involved with one fashion label, it is understood these payments were related only to his contract as a footballer.

The total value of Keogh's salary is believed to be between $300,000 and $350,000 a season, yet it is understood the club recorded his salary as $150,000 in its reportings to the FFA.

Perth Glory were already spending close to the salary cap limit of $2.55 million a season, deeming the alleged additional payments as a significant breach of the limit.

Keogh signed a two-year deal with the club on May 30, with an option for the Glory to extend the contract for a third season. The Republic of Ireland international has been central to Perth's success this campaign: he was their top scorer as they led the league for the first half of the season, reached the FFA Cup final and now sit in fourth position.

Keogh's signing precedes Perth Glory moving Nebojsa Marinkovic and Michael Thwaite into marquee positions outside of the salary cap to avoid breaching the limit.

"Football Federation Australia today issued Perth Glory Football Club with a second Show Cause notice relating to alleged breaches of the Hyundai A-League's Player Contract Regulations ('salary cap')," an FFA statement read.

"The second notice is in relation to the current season. The alleged breaches involve failure to disclose reportable payments and exceeding the salary cap. The 'failure to disclose' breaches involve:

• Payments outside of the Standard Player Contract,

• Payments to a player's family member,

• Payments of player agents' fees,

• Payment of a third party sponsorship,

• Pre-payment to a player,

• Payment of travel costs,

• Accommodation allowances,

• Provision of motor vehicles.

"The value of the undisclosed payments and benefits involved in the alleged breaches would place Perth Glory significantly in excess of the allowable salary cap of $2.55m."

The revelations of payments made outside of the cap were found during an FFA investigation into allegations of Perth's salary cap breaches, prompted by a Fairfax Media report in December last year. The governing body undertook a forensic audit of Glory's accounts and player payment methods, uncovering what is the most serious alleged salary cap breach in the history of the A-League.

The club will now has to explain its actions to the governing body.

Perth's management will be given up to one week to respond to the notice explaining their actions before they face the possibility of hefty sanctions, which could significantly effect their final finish on the A-League table just weeks before the finals series begins.

Sources close to the club suggest senior officials, players and directors were interviewed by the FFA investigation team, led by A-League chief Damien De Bohun, since the start of the year. The latest show-cause notice follows an earlier notice issued in February relating to the club's failure to report players' accommodation, player-agent fees and club vehicles issued to players in the salary cap for the past three seasons.

While such benefits are permitted within the strict reporting guidelines of the salary cap, the club is required to report all such benefits to the FFA throughout the season.

Perth Glory are alleged to have provided accommodation for several players during the past three seasons. A Fairfax Media investigation revealed the club failed to declare up to $50,602 in player agent fees in the 2012-13 season, which is required by the salary cap.