The Commonwealth Ombudsman has found the federal fisheries authority breached the Fisheries Act in the process of setting the quota for the controversial super trawler.

In a letter released by federal independent MP Andrew Wilkie, Senior Assistant Ombudsman Rodney Lee Walsh said the Australian Fisheries Management Authority (AFMA) admitted to breaching a section of the act.

The breach occurred in February, when Seafish Tasmania director Gerry Geen declared a conflict interest to a meeting of the assessment group that sets quotas for the small pelagic fishery.

Mr Geen was allowed to remain in the meeting.

His presence has been a point of contention for recreational fishers and green groups who opposed his company's controversial super trawler, now called the Abel Tasman.

Mr Wilkie lodged a complaint to the Commonwealth Ombudsman on behalf of the fishers' concerns.

The Assistant Ombudsman says other matters have also come up during the investigation and these are still being considered.

Destructive or sustainable? The size of the Margiris, now named Abel Tasman, has sparked fears it will decimate fish stocks. But Australia's fishing regulator says the trawler's quota is based on sound science. So will the super trawler devastate a region, or will its catch be a drop in the ocean?

Mr Wilkie says that is cause for concern.

"Clearly we have a broader problem within AFMA. Clearly there are systemic problems," he said.

Both the Ombudsman and AFMA have been contacted for comment.

Yesterday, new laws aimed at stopping the super trawler from fishing in Commonwealth waters narrowly passed the Lower House.

The Federal Opposition voted against the bill but it passed with the support of most crossbench MPs, including Rob Oakeshott, who had previously voiced concerns about the legislation.

The bill will now be considered by the Senate next week.

Once the legislation passes the Senate, the trawler will be prevented from fishing in Australian waters for up to two years while extra scientific research is carried out.

Environment Minister Tony Burke rushed legislation into Parliament on Tuesday in the face of a strong public campaign against the super trawler.