Basketball Australia has rejected claims from Philippines coach Chot Reyes that Boomers players sparked tensions by "hitting" opponents during the warm-up before their World Cup qualifier.
But CEO Anthony Moore admits it "wasn't the smartest move" by team officials to remove floor decals they believed had posed a threat to player safety.
Speaking to reporters after Monday night's brawl, Reyes accused Australian centre Daniel Kickert of striking four Filipino players before the match had even started and blamed him for "triggering" the all-in fight by elbowing Roger Pogoy in the face in the third quarter.
While condemning Kickert's in-game actions as "unsavoury", Moore said nothing of the sort had happened during the warm-up.
"We absolutely refute that. It's a conversation we've had with team management," he told reporters in Brisbane on Tuesday.
However, Moore confirmed the Boomers may have unwittingly riled the hosts by tearing up advertising boards that players had slipped on the day before the game.
Australian basketball great Shane Heal, who was commentating for Fox Sports, told Channel Seven the actions were taken to be "disrespectful" by the Philippines.
Moore said Basketball Australia later apologised to the Philippines Basketball Association.
"We had a team shootaround the day before, floor decals are always something that you look at," he said.
"We trained, had numerous players fall and fall heavily and our team management undertook a course of action that we actually apologised for. We ripped the decals up.
"That wasn't the smartest move we made.
"There's no doubt that heightened the issue, but that was more from an administrator, federation-to-federation part as opposed to players."
Meanwhile, Moore, like many observers, was left puzzled by the actions of the Philippines team straight after the fighting stopped.
As FIBA officials took stock and deliberated over whether the game should continue, several Filipino players gathered to take a group selfie.
"I thought it was pretty odd, to be in a position where you've been in a major altercation and then to be seemingly enjoying the moment. I found that very strange," he said.