A study on the effectiveness of commercial whale alarms in deterring the ocean giants from fishing nets and lines measured no response from migrating humpback whales.

Rob Harcourt, the research leader from Macquarie University, said he was surprised by the research findings because the devices had been shown to work in other parts of the world.

"The fishermen swear by them in the north Atlantic and north Pacific, so I thought we'd see the whales at least slow down or alter what they were doing, but we just didn't detect anything at all,'' he said.

Some whales even swam right over the top of the alarm, which was positioned off Botany Bay, in the middle of the "humpback highway'' the animals used to travel north, Professor Harcourt said.

"If there was a net there they would have run straight into it,'' he said.

From the lookout at Cape Solander, research assistant Vanessa Pirotta tracked the speed, dive behaviour and direction of 137 whales over two months in 2012.

"As the researcher, I was blind to whether the alarm was on or off,'' she said.

There was, however, no difference in the whale's behaviour whether the alarm was on or off.

Ms Pirotta said it was not just the long lines and gill nets that snared whales. Single lobster and crab pods were also a threat, as were shark nets designed to protect swimmers.

"Last year, off Mona Vale, there was a young humpback calf entangled in a shark net fitted with these devices,'' said Ms Pirotta. "It died from that event."

Professor Harcourt said in the case of some whales, such as the endangered south right whale, entanglement had prevented their recovery after whaling was banned.

"Every single adult [southern right] female you kill potentially is enough to reverse their recovery because their numbers are so low,'' Professor Harcourt said.

Apart from the impact on the animals, whale entanglements costs governments and fishermen millions of dollars each year.

The results of the study – a joint project between Macquarie University, NSW Department of Primary Industries and Taronga Conservation Society – were published in the scientific journal Endangered Species Research.

Ms Pirotta and the group have since deployed a bigger, more powerful sweeping alarm that was loud enough for the whales to hear above the noise generated by ships and other animals in Botany Bay.

"We're still analysing the data, but we haven't detected an effect yet,'' Professor Harcourt said.