The House of Representatives has narrowly passed new laws aimed at stopping a super trawler from fishing in Commonwealth waters.

The 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.

As part of the last-minute negotiations, the Government agreed to several amendments to ensure the legislation would not affect recreational fishing and to impose a 12-month sunset clause on the minister's powers to restrict fishing activities.

There will also be a thorough review of fishing laws to make sure regulators have enough power to adequately deal with the latest scientific assessments of fishing stocks.

"I accept now that the Fisheries Management Act will be root-and-branch gone through and that this inquiry will matter," Mr Oakeshott told Parliament.

"I am pleased that we are now going to tidy up the science and make the science matter, and make the process matter, so that in the future we don't have weeks like the one we've had this week happen again."

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?

Environment Minister Tony Burke rushed legislation into Parliament on Tuesday in the face of a strong public campaign against the super trawler Abel Tasman, formerly called the Margiris.

The ship was brought to Australia as part of a joint venture between Seafish Tasmania, which has a fishing quota of almost 18,000 tonnes, and a Dutch company.

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.

Mr Burke had earlier told Parliament that the Australian Fisheries Management Authority (AFMA) had conceded errors in implementing the existing legislation and he therefore did not have confidence in its assessment of the trawler's environmental impact.

"Whether it be because of their legislation or because of their own actions, I do not believe they (AFMA) have been precautionary enough," Mr Burke said.

"AFMA themselves, in the last 24 hours, have reported to the Government legal advice that some aspects of the Act they have been implementing incorrectly."

The Government did not detail the nature of the error and instead referred inquiries to AFMA, which told the ABC it could not disclose the nature of its legal advice.

Independent MP Tony Windsor had previously warned the Government he would vote against the legislation if he was rushed into a decision and expressed concern that it would set a bad precedent for other government intervention.

He ended up siding with the Coalition to oppose the bill.

'Fatal flaw'

Opposition environment spokesman Greg Hunt says there remains a "fatal flaw" in the legislation that will cause uncertainty for the fishing industry.

"The Government has today handed itself extraordinary powers," he said in a statement.

"The fatal flaw in today's fisheries amendment to the Federal Environment Act gives the Government arbitrary power, without warning or evidence, to immediately close any new small family fishing operation anywhere in Australia."

Mr Hunt said the Government should now offer compensation to the 50 workers affected by the decision.

The Greens made a last-ditch effort to ban all super trawlers, but that was voted down. Even so, they are pleased with the outcome.

"Our preferred result would have been to have had a blanket ban on such vessels and a cancellation of the existing quotas while more research was undertaken," Greens leader Christine Milne said.

"At least we now have some clear water to sit back and take a good look at how AFMA has handled this issue."