There are calls for the Federal Government to develop a long-term strategy to protect threatened marine species from commercial fishing.

Every year thousands of marine mammals are killed as bycatch, the numbers are recorded and published online, but interest groups believe there is no strategy to reduce the number of deaths.

The Australian Fisheries Management Authority (AFMA) publishes a quarterly report detailing how many animals have been killed in Commonwealth waters.

In the Eastern Tuna and Billfish fishery off Australia's east coast the numbers fluctuate from year to year.

In one quarter, from April-June 2012, 776 marine animals were killed, including turtles and birds.

In the same quarter in 2014 there were 414 deaths, and this year there were 515.

The Australian Marine Conservation Society's Tooni Mahto said the numbers were unacceptable.

"Bycatch in Australian fisheries is the number one problem that Australian fisheries face," she said.

"That's not an acceptable situation, we want to see the bigger picture thinking about reducing the impact of Australian Fisheries on marine wildlife."

Ms Mahto believes there is no long-term strategy to bring numbers down.

"What we would like to see really is some kind of analysis as to whether the amount of bycatch is being reduced over time, whether there are particular species that need far more attention, whether there are particular fisheries that need more attention," she said.

"What we would really like to see is an overarching commitment from the Australian Government and from the fishing industry, to work proactively and strategically to really try and reduce that level of bycatch."

The Australian Fisheries Management Authority declined to be interviewed on the issue, but instead issued a statement:

"The Commonwealth Policy on Fisheries Bycatch is in place to ensure that direct and indirect impacts on marine systems are taken into account and managed accordingly," the statement read.

"Each Commonwealth fishery also has in place a range of requirements to minimise the risk of bycatch."

Questions raised over trawler kill reporting

In the Small Pelagic Fishery, which spans across Australia's south has seen a spike in the number of animals killed this year.

Small Pelagic Fishery bycatch In all of 2012 - no protected species killed as bycatch

In all of 2012 - no protected species killed as bycatch In all of 2014 - no protected species killed as bycatch

In all of 2014 - no protected species killed as bycatch April to June 2015 - 26 protected species killed as bycatch

The jump is due to the fishing operations of the controversial trawler the Geelong Star.

The number of protected species deaths revealed in the quarterly reports differs from what has been posted by the Australian Fisheries Management Authority's website.

In late April, AFMA posted a press release online revealing the Geelong Star had killed four dolphins and two seals.

In early May the public was notified of another four dolphins and two seals, and in June one more dolphin.

Since the Geelong Star started fishing, AFMA has revealed the deaths of nine dolphins and four seals.

The 95-metre long Geelong Star has reignited debate about the overfishing capacity of large trawlers. ( ABC News: Mark Bennett )

But actual numbers for the Geelong Star are 12 seals, nine dolphins, three shortfin mako sharks, two shy albatross and one unknown, a total of 26, according to the AFMA report.

Alistair Graham from the Humane Society International's Australia branch is unimpressed by the discrepancy.

"They're making it up as they go along," he said.

"When it comes to cock up and conspiracy I'm a great believer in cock up. I mean, these guys just have no idea how to manage this issue."

The Australian Fisheries Management Authority again declined to be interviewed, but in a statement said:

"The Geelong Star is just one of the 300 plus vessels operating in Commonwealth fisheries."

"All of the reported threatened, endangered and protected species interactions of each of these vessels are published publicly per fishery on a quarterly basis on AFMA's website.

"This is in line with requirements and procedures agreed between the Department of the Environment and AFMA.

"This approach is regarded as reasonable and feasible given data receipt, processing and verification times."