The deaths in the ship's trawl net off south-eastern Australia were disclosed by the Australian Fisheries Management Authority (AFMA) on Tuesday night.

They came despite the installation of a marine mammal escape device in the big net of the Dutch-owned ship, which is opposed by a coalition of environmentalists and recreational fishers.

Geelong Star is trawling for 16,500 tonnes of redbait and jack mackerel using a 80 metre wide, and 35 metre high net, in the same offshore small pelagic fishery that was to have been fished by the banned supertrawler Margiris.

The "outrageous" toll  of dolphins and seals spurred the Stop the Trawler Alliance to call for an immediate halt to fishing, and a return to port by the Geelong Star.

"This is extraordinary news," said the alliance's Rebecca Hubbard.

"AFMA has repeatedly given assurances that this huge factory trawler is nothing new and does not pose an unacceptable threat to our marine life," Ms Hubbard said.

"I don't think the public will believe that now," she said.

"We expect the vessel to be docked immediately, and for Prime Minister Tony Abbott and Environment Minister Greg Hunt to stop it fishing further."

AFMA's chief executive, James Findlay, said the Geelong Star would be required to return to port if further dolphins were killed.

"The sustainability of the entire marine ecosystem, including marine mammals, is a priority for AFMA and we take any marine mammal mortality very seriously," Dr Findlay said.

Additional measures would be imposed on the Geelong Star including modifications to the net's escape device, and day-time fishing only, Dr Findlay said.

The Small Pelagic Fishery Industry Association's chairman, Grahame Turk, said AFMA's swift response to the mortalities from the Geelong Star showed the regulatory system was working.

Mr Turk said a supplier had been engaged to design and supply a barrier net to fit across the trawl net's mouth, to prevent the entry of dolphins.

"Marine mammal interactions regrettably sometimes occur in mid-water trawl operations in Australian waters," Mr Turk said.

"As a freezer trawler, the Geelong Star has the ability to move to new fishing grounds away from where dolphins have been sighted, reducing the likelihood of future interactions."