Scientists have found that clever killer and sperm whales have discovered the convenience of take-away meals – namely learning how to suck trapped fish off commercial fishing lines.

"I was pretty amazed," Deakin University marine biologist Paul Tixier said. "We thought whales were highly specialised animals … But here we have a human activity and the whales have switched their behaviour to take advantage of it."

The whales' learned behaviour could mean some fish species, such as the highly regulated Patagonian toothfish and blue-eye trevalla, are being overfished as the whales' sizeable share is not included in strict quotas set by authorities.

In the case of killer whales, blue-eye trevalla is not a typical prey as the whales can only dive to 500 metres and the fish are found in deeper waters. But long-line fishing appears to have added the fish to the whales' diet.

It's an unexpected side effect of commercial long-line fishing, which has largely replaced trawling as a more sustainable, environmentally friendly option because it targets species and reduces bycatch.

Dr Tixier said there was no way of estimating how many fish the whales were removing from the long lines as the whales often made off with the entire fish.

Sperm and killer whales are highly social animals and the learned behaviour would be quickly shared within family groups and beyond, Dr Tixier said. He said for this reason it was vital researchers intervened to tackle the problem before too much damage to the marine ecosystem was done.

The discovery will have implications for the viability of the fish species preyed upon and the fishing industry. It could also affect the savvy whales, which could become over-reliant on line fishing and lose their ability to effectively hunt prey.

The behaviour was first noted in the French territory near the Kerguelen and Crozet islands, in the remote subantarctic waters below Africa and Australia. The area is not far from Australia's Heard and McDonald islands, which lie 4000 kilometres south-west of Perth.

With Deakin University colleague John Arnould, Dr Tixier will begin a four-year research project this month which will use satellite tags to track whales' movements in Australian waters. Skin samples will be taken to reveal each whale's isotopic signature. This data will provide insights into each animal's diet and the area in which they are feeding.

"The idea at the end is to find a solution to minimise the interaction between commercial fishing vessels and whales," he said.

Professor Arnould said the research will focus on the waters off Heard and McDonald islands where sperm whales and Patagonian toothfish are found, as well as waters between Eden, NSW, and Port Lincoln, South Australia, where killer whales and blue-eye trevalla are found.

"This suggests our fishing models are off and that has implications for the whole ecosystem," Professor Arnould said.