Federal Environment Minister Greg Hunt has described the deaths of marine mammals in the net of a factory fishing trawler as "unacceptable and outrageous".

In two fishing trips in Australian waters the 95-metre ship has caught and killed eight dolphins and four seals in its net.

This week, the Australian Fisheries Management Authority (AFMA) said the killings of such marine animals were was inevitable but everything possible was being done to prevent them.

Stricter controls had been placed on the trawler after it reported catching four dolphins and two seals on its first fishing trip in Australian waters.

On Saturday the Geelong Star returned to its home port in Victoria after reporting the catch of four more dolphins.

There has been widespread backlash from both environmental groups and recreational fishers.

Mr Hunt released a statement Sunday morning in which he said he was "absolutely appalled" by the news.

The statement said Mr Hunt would be writing to both the Australian Fisheries Management Authority and to Tasmanian senator and Parliamentary Secretary for Fisheries, Richard Colbeck, who has been vocal in his support of the science behind the trawler's fishing practices.

Senator Colbeck has released a statement in response:

The death of more marine mammals is very bad news and is not welcomed by anyone. The decision of the vessel operators to voluntarily return to port is appreciated. The Government has confidence in AFMA as fisheries managers - AFMA has an excellent track record of managing similar issues in other Australian fisheries. We understand that further work is to be done on marine mammal exclusion devices, this has the potential to benefit fisheries management more broadly given there are a number of other fisheries that use similar fishing methods.

Greens Senator Peter Whish-Wilson has called on the Federal Government to immediately revoke the Geelong Star's fishing licence and cancel its fishing management plan.

"They've failed twice. The regulator has failed in its job to protect dolphins and seals and who knows whatever other marine life and the boat needs to go home," he said.

The trawler, operated by Seafish Tasmania, has permission to catch 16,500 tonnes of pelagic fish a year.

Tasmanian fisher Tyson Clements said he wanted Mr Hunt to act.

"I'm calling on the environment Minister to put a stop to this fishing in the small pelagic fishery at once," he said.

"We don't want to see these deaths of dolphins. Recreational fishermen do not kill dolphins and we certainly do not want any dolphins hurt in this process.

"This fishing is wrong."

The Geelong Star returned to its home port of Geelong voluntarily.

Seafish Tasmania has declined an interview.