Roar's youth team, which plays in the second-tier league, has withdrawn from away games against Cairns-based Far North Queensland FC on 11July and Townsville-based Northern Fury on 18 July, citing increased training demands ahead of its glamour match against Liverpool on July 17.
However, it is understood the real reason is that Roar - currently crippled by a financial crisis and unable to pay players and staff - cannot meet costs for flights and accommodation.
Rival clubs are furious at the decision, which has been seen as hugely disrespectful to the NPL and damaging to the competition's integrity, with both forfeits to be recorded as 3-0 defeats.
Football Queensland chief executive Geoff Foster said he was unhappy but accepts Brisbane's justification.
"They certainly understand how seriously we treat the league and the level of disappointment we're currently feeling," Foster told AAP.
"We will share our disappointment with FFA."
Football Federation Australia (FFA) declined to comment, saying it was a matter between the club and Football Queensland, while Roar had no further comment beyond .
"The Roar first-team squad, which includes several players recently promoted from the club's Youth ranks, resumes training on 1 July," the statement read.
"As well as an intensive fitness program, the short preparation for the Liverpool game is expected to also include an in-house 11-versus-11 training match which would be difficult to stage with players travelling out of Brisbane twice in seven days."
It comes after the state of Brisbane's perilous finances were laid bare on Tuesday by a leaked e-mail to staff, which claimed owners The Bakrie Group had promised to refinance the club with a $3.5 million cash injection.
However, the money is yet to arrive, leading to the non-payment of wages which were due on 15 June.
Both FFA and the A-League players' union described the situation as "unacceptable".
It may not get better in a hurry - the club has significant debts owing to a string of creditors, its sponsorship with The Coffee Club is set to expire on Tuesday and sacked coach Mike Mulvey is poised to take legal action with Roar yet to pay out the rest of his three-year contract.
Meanwhile, Roar is scrambling to find a suitable training venue for when players return for pre-season duty next week.
The club's contract with the Queensland Rugby Union to train at Ballymore has expired and Brisbane's new home base, Perry Park, is not in a good enough condition to deal with any further traffic.
