It is understood crews have freed a whale entangled in shark control equipment on Tuesday off Marcoola Beach on the Sunshine Coast, about an hour-and-a-half north of Brisbane.
Another whale is entangled in nets off Kirra on the Gold Coast, environmental groups say.
Both are believed to be humpbacks on their annual winter migration.
"Today there have been two confirmed whale entanglements in shark nets off Queensland's coast, in addition to the two already confirmed in the past month," Lawrence Chlebeck, a marine biologist with Humane Society International, said.
"Sadly the public can only watch on in dismay.
"The minister's own scientific experts advised him to trial a removal of the nets during the whale migration season.
"Each year that the advice is not acted on will only see more whales entangled."
Queensland's shark control program includes nets and drumlines at 86 beaches. Trials are underway for new technology including drones and catch-alert 'smart' drum lines.
A Shark Control Program Working Group supported trialling the replacement of some nets with drumlines in 2020, but Queensland Fisheries Minister Mark Furner says human life will always come first.
"We are investing in research and technology, but we simply will not make changes to the program unless we are convinced they are safe in Queensland conditions," he said in a statement.
"Our contractors and marine animal rescue teams do amazing work to minimise impacts on other marine life, while maintaining a program that has helped to keep Queenslanders safe since 1962."
Sea Shepherd Australia is also calling on the state government to replace shark nets with modern alternatives
"Whales are one of the most iconic marine species on this planet, and the feats they make as they circumnavigate the world are beyond astounding," campaigner Lauren Sandeman said.
"By keeping shark nets in their path against scientific advice, each year we purposely endanger them with a slow and gruelling death."
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