The humpback whales were on their annual winter journey along eastern Australia when they became entangled off the Gold and Sunshine coasts.

Sunshine Coast crews were alerted to an animal in distress off Marcoola about 8am on Tuesday. The whale was freed three-and-a-half hours later.

The rescue off Kirra on the Gold Coast took about two hours, with crews alerted just before 10am and releasing the animal about midday.

Both rescues followed reports to the 24-hour Shark Hotline.

An estimated 40,000 whales migrate along Queensland's coastline each year, with six entanglements reported on average, Fisheries Queensland says.

Since 2013, there have been 57 entanglements, with 55 whales released alive.

Queensland's shark control program includes nets and drumlines at 86 beaches. Trials are under way for new technology including drones and catch-alert "smart" drumlines.

Electronic warning devices such as acoustic pingers are also used to alert whales and dolphins of nearby nets.

While environmental groups welcome the new technology, they say the use of shark nets goes against the science.

"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," said Lawrence Chlebeck, a marine biologist with Humane Society International.

"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."

A Shark Control Program Working Group supported trialling the replacement of some nets with drumlines in 2020, but Queensland Fisheries Minister Mark Furner said human life would 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."

Australian Associated Press