It was revealed on Tuesday that payments scheduled to arrive on 15 June had not yet been made as the club continues to experience financial difficulties.
FFA and PFA each described the situation as "unacceptable".
"Football Federation Australia is aware that Brisbane Roar has some financial issues," a spokesperson for FFA said.
"FFA stresses that the non-payment of players and staff is unacceptable and needs to be resolved urgently by Brisbane Roar."
PFA issued a statement that said the latest development had the effect of "further highlighting the players' concerns regarding the good governance of the A-League".
"Professional Footballers Australia continues to monitor the situation of non-payment of players’ wages at the Brisbane Roar," the statement read.
"This is a matter of serious concern and the PFA has been seeking an immediate resolution. The non-payment of players is completely unacceptable, with the situation at the Roar further highlighting the players’ concerns regarding the good governance of the A-League.
"Over the history of the A-League players have consistently been the victims of poor governance and the PFA will continue to seek reforms to ensure the reputation of Australian football is enhanced and that its governance is the world's best.
"The security of player payments is fundamental to this and the players will continue to advocate for contract security to ensure that no players goes unpaid.
"The PFA will continue to support the players during this difficult time and commends them on their professionalism in the face of adversity."
The FourFourTwo website also reported that an internal letter sent to Roar staff said the club was sweating on a further cash injection of $3.5 million from the Bakrie Group, it's Indonesian-based owners.
It also reported the letter saying that in the wake of Roar managing director Sean Dobson's departure from the club last month "very serious financial liabilities" had been discovered.
Roar, which has won three of the last five A-League championships, recently appointed former Socceroos striker John Aloisi as its new coach, on a two-year deal.
As of Tuesday evening there had been no official reaction from Roar regarding the pay situation, but the club did issue a media release announcing the appointment of former Australia and Roar defender Craig Moore as the club's football operations manager.
Aloisi was quoted in the release, saying: "Craig has a wealth of experience in football and a first-hand understanding of what it means to play for the Roar.
"He will work closely with me as Football Operations Manager.
"His football knowledge and his love for the club will be invaluable as we transition to a new era and rebuild the Roar to challenge for honours again."
Moore said it was "great to be back at the club at such an exciting time", adding: "I aim to support John and oversee the structure and operations of the club’s football department."
