More than 1600 individual protected birds or marine life were recorded as dead as a result of being netted, hooked or entangled in commercial fishing operations.

The preliminary protected species interactions quarterly report for July to September 2016 states 59 seals died, along with six dolphins, 10 albatross, three turtles, 196 seahorse, more than 300 sharks and almost 1000 sea snakes. This was across all Commonwealth fisheries.

In the small pelagic fishery, 31 more deaths were recorded in the most recent report compared with the same period last year, including 19 fur seals. A spokesman for the Australian Fishing Management Authority said fishing activity was lower in the comparative period last year.

However, the spokesman said the existence of the Geelong Star super trawler in Australian waters would have had an impact on the bycatch numbers.

"The other vessels fishing in the small pelagic fishery use a different fishing method, purse seine, and commercially fish Australian sardine and some blue mackerel," the spokesman said.

"The Geelong Star commercially fished for redbait, jack mackerel and blue mackerel. The Geelong Star's bycatch numbers reflect its larger fishing quota and catch than other SPF vessels which have much smaller quota and catch."

The spokesman said while the numbers would have increased due to the vessel, the Geelong Star's bycatch was about 2 per cent by weight of the total catch.

"This is low when compared to many other fishing operations," the spokesman said.

The Geelong Star recently left Australian waters, which was confirmed on the eve of the Senate inquiry report being handed down into its operation.

The spokesman said the authority was always looking at ways to minimise and avoid interactions with protected species.

"All fishing operations, including recreational and commercial, pose risks to protected species in order to put Australian seafood on our tables.

"AFMA has a comprehensive monitoring system for protected species interactions in Commonwealth fisheries.

"In addition, the fishing industry continually works with scientists, government regulators and other fishery stakeholders to implement new technology to reduce protected species interactions."

The report, released on Wednesday, is required under a memorandum of understanding between the Australian Fishing Management Authority and the Department of Environment and Energy.

It collates the information from the more than 300 Commonwealth fishing vessels on a quarterly basis.