The NBL has been dogged by uncertainty over teams throughout its history, with the Crocodiles the latest in a long line of clubs to fold.
NBL general manager Jeremy Loeliger said the decision to pull the plug on the Crocodiles was in the league's best interest.
"In order for the NBL to be one of the strongest basketball leagues in the world, we must have teams that are commercially sustainable - we cannot allow our players, fans or sponsors to have any lingering doubt as to the longevity of our clubs," Loeliger said.
"There is no point in trying to sustain a club that has itself resolved that it cannot survive in its home town."
Queensland will still be represented in the 2016-17 season by the Cairns Taipans and a revived Brisbane Bullets in what will remain an eight-team competition.
The NBL has confirmed all financial commitments made by the club for the 2015-16 season will be honoured.
- AAP