The report, entitled 'Independent observations of catches and subsurface mitigation efficiencies of modified trawl nets for endangered, threatened and protected megafauna bycatch in the Pilbara Fish Trawl Fishery', was released in 2014 - two years after the monitoring was done by Fisheries. The bottlenose dolphin, or Tursiops truncatus, a cetacean, is protected under Australian laws. Credit:Simon Allen It was not peer reviewed but featured a net technician from MG Kailis Group - a major player in Australia's fishing industry which also operates a boat in the Pilbara Trawl - as one of the report's contributors. The other authors were scientists and managers from Fisheries. The report was then used to gain approval from the federal Department of Environment and export accreditation under Wildlife Trade Operation regulations.

Independent scientists from Murdoch University attempted to warn the Minister for Environment, Greg Hunt, that the report contained information that was "misleading", "inaccurate" or "incomplete". Fisheries refused to directly answer questions from Fairfax Media concerning claims that the report was misleading, but would not deny numerous allegations levelled against the report and its authors. "The Department of Fisheries works in a cooperative way with the commercial fishing industry to better understand the impacts of different fishing practices," according to Dr Brett Molony from Fisheries, who was also one of the report's authors. But, despite acknowledging that close interaction between industry and Fisheries, Dr Molony maintained the report was independent. "With regard to the independence of the research, the information and findings were reviewed by the Commonwealth Department of the Environment and posted on their website for public review," Dr Molony said.

But the Murdoch University scientists stated in a report to Greg Hunt "[u]se of the term "independent" in the title and throughout the report is misleading". "A survey of bycatch… ...completed by staff scientists and managers of the Department of Fisheries and an employee in the [Pilbara Trawl fishery] is not 'independent' and this conflict of interest should perhaps have been declared." The Pilbara fishery is one of the richest fishing areas in Australia, worth millions of dollars, providing a lucrative catch of bream, red snapper, red emperor, trevally and cod in waters up to 100-metres deep for domestic consumption. Two vessels currently trawl in the fishery - one owned by MG Kailis based in Exmouth, the other by Westmore Seafoods operating from Point Samson, about 1500 kilometres north of Perth. The boats cover an area of about 23,000 square kilometres, stretching from Dampier to Port Hedland.

Trawl fishing in the Pilbara region was identified as a threat to the local bottlenose dolphin population when Fisheries began assessing the impact of fishing on marine life in the area more than a decade ago. In 2009, the federal Department for Environment warned Fisheries in a letter that it had concerns over the lack of progress in the Pilbara trawl, including the threat to endangered sawfish, turtles and dolphin deaths. "In light of our continuing concerns, unless significant progress is made to address these, we will find it difficult in future assessments to continue to find that this fishery meets the sustainability requirements of the EPBC Act [Environment Protection and Biodiversity Conservation Act 1999] as supported by the Guidelines," stated Nigel Routh, a delegate for a former Minister for Environment. As the letter was penned, more than five years ago, the Pilbara trawl was a catch declining in marketable produce but continuing to threaten the bottlenose dolphin. In 1996, the fishery caught 3,200 tonnes but, by 2013, that figure had dropped to 1,074 tonnes, according to Fisheries.

Numerous boats previously trawled the area but the declining catch and ongoing dolphin deaths prompted several vessels to withdraw, leaving two remaining. Despite more than a decade of high-level concerns and warnings amid a declining catch, the dolphin deaths continued. Peer-reviewed research by scientists at Murdoch University found that 50 or more protected bottlenose dolphins a year were killed as bycatch in the trawl. But Dr Molony claimed less than 25 dolphins a year die as a result of being caught up and suffocating in the Pilbara trawl nets. Fairfax Media has been told that Fisheries has video footage showing how dolphins suffer traumatic deaths as they struggle to break free from entanglement in the nets slowly dragged along by the trawlers.

Dr Molony also previously attempted to play down the significance of the protected dolphin deaths, referring to the dolphin species as one of "least concern" with an estimated population of 600,000. But this figure represents a global estimate of the bottlenose dolphin species as a whole – there are only a few thousand dolphins in the area of the Pilbara fishery. No one knows how many there used to be. Fishers have attempted to divert blame for the dolphin deaths to the Japanese, Taiwanese and Koreans who stopped fishing in the region decades ago. Gary Kessell, owner of Westmore Seafoods, previously told Fairfax Media: "We're just the locals, the Johnny-come-lately."

Dr Molony also noted the impact that foreign fishers have had on the dolphin population. "The stock of bottlenose dolphins has been interacting with trawlers since at least the 1960s," he said. "Combined with fishing by foreign fleets up until the mid-1980s, thousands of mortalities were reported." Fisheries was also told to prepare a code of conduct for fishers in the region aimed at reducing dolphin deaths following studies in 2012. But the code of conduct, a voluntary set of guidelines, is not due to be implemented until 2017 - by which time dozens more dolphins are expected to die in the nets.

Federal Environment Minister Greg Hunt declined to be interviewed. But a spokesperson for Mr Hunt said "these issues were considered in the assessment of the Minister's decision". "The Minister placed conditions to protect dolphins and sawfish on the EPBC Act accreditations." Helene Marsh, Distinguished Professor of Environmental Science at James Cook University, where Dr Molony studied, has suggested that Fisheries scientists should take a closer look at the studies produced by Murdoch University. "Interpretation of the significance of their results would be enhanced by reference to two relevant papers published in the peer-reviewed literature since the report was released and Dr Simon Allen's 2015 PhD thesis," she said.

"I suggest that it would be timely for an independently facilitated workshop of government and university scientists to be convened with the aim of producing a synthesis report." The bottlenose dolphin, or Tursiops truncatus, a cetacean, is protected under Australian laws. Protected and critically endangered sawfish are also still being caught in the Pilbara Trawl Fishery, prompting concern from scientists. Follow WAtoday on Twitter