The Dutch super trawler Margiris is the target of escalating opposition ahead of its arrival in Australian waters.
The Greens and the independent MP Andrew Wilkie have each launched attempts to overthrow a federal government decision on fishing quotas that the Margiris is to use.
Public protest shifted to Canberra today, where a 35,000-name petition was lodged against the ship at a rally by environmentalists and recreational fishermen.
The 9500 tonne Margiris, which will be the largest trawler ever to fish Australian waters, is due to arrive later this month, according to a spokesman for its Australian joint venturer, Seafish Tasmania.
The ship needs to be re-registered as Australian before it can begin trawling for redbait and mackerel between the Tasman Sea and Western Australia.
The Commonwealth Ombudsman today confirmed it was inquiring into the process used to reach the quotas after Mr Wilkie said it appeared the Australian Fisheries Management Authority had not followed the law.
"My office is looking at Mr Wilkie's complaint and we have asked AFMA for more information about its administrative processes," acting Ombudsman Alison Larkins said. "At this stage, however, we have not formally begun an investigation or made any assessment regarding AFMA's actions," she said.
Mr Wilkie said a meeting with AFMA had heightened his concerns.
"AFMA yesterday morning admitted that there were defects in the assessment process and acknowledged it needed to tighten up its processes," he said. "We need to get to the bottom of this before the federal government allows this factory ship to start fishing in Australian waters."
An AFMA spokeswoman said: "If the Ombudsman does decide to investigate, AFMA welcomes the Ombudsman's scrutiny and remains confident that the total allowable catches have been lawfully made."
Greens Senator Peter Whish-Wilson is also attacking the AFMA process over concerns that the Margiris operation will lead to localised depletion of fish.
Senator Whish-Wilson said he was convinced the scientific work on the quotas did not stack up, and he is to move in the Senate that the decision on the trawler's quotas be reversed.
Fisheries Minister Joe Ludwig has formed a working group to examine licence conditions for the Margiris.
A spokesman for the Department of Agriculture, Forests and Fisheries, said: “The working group is making progress and is considering a range of issues, including localised depletion.”
Supporters of the venture say the quotas are conservative and sustainable. Prime Minister Julia Gillard has defended AFMA's processes, and the venture has backing from both major parties.
The global Dutch company Parlevliet & Van der Plas is joining some key figures in Australian and New Zealand fishing in the venture. Apart from local director Gerry Geen, Seafish Tasmania's directors include Auckland multi-millionaire Peter Simunovich and long-time Australian trawlerman Joseph Pirrello, according to ASIC records.
Mr Simunovich's family made its fortune in the New Zealand scampi trade. Mr Pirrello was involved in trawling for several species including orange roughy in the 1990s, according to parliamentary records.