The bill passed on voices this afternoon, with the government's amendments passing 62 votes to 60.

The super trawler ban earned the support of independents Bob Katter, Andrew Wilkie, Rob Oakeshott and Craig Thomson, as well as Greens MP Adam Bandt.

But independent Tony Windsor sided with the opposition against the ban after earlier expressing concerns that his decision had been rushed.

The government announced the super trawler ban earlier this week, with Environment Minister Tony Burke arguing that further scientific assessments of the FV Abel Tasman environmental impact needed to be carried out.

Labor also announced the government would carry out a ''root and branch review'' of fisheries management law in response to concerns about the 18,000-tonne fish quota given by fisheries authorities to the operator of the 142-metre, Dutch-owned ship.

This afternoon, a Greens amendment to ban all super trawlers permanently was lost. But the bill passed with amendments from Mr Thomson, which narrowed the scope of the ban to ''commercial'' fishing activities.

It also passed with an amendment from Mr Oakeshott, placing a sunset clause on the new extended powers of the Environment and Fisheries ministers.

As of yesterday, the government's push for a two-year ban on the controversial Abel Tasman faced a stormy ride in Parliament, with the Coalition saying it would oppose the legislation.

Mr Oakeshott called it an ''attack on science'', with fellow crossbenchers Mr Thomson and Mr Windsor also expressing reservations.

Earlier today, Greens leader Christine Milne said independent MPs were falling for Coalition ''red herrings'' and needed to pass laws banning the super trawler as soon as possible.

''The Greens are calling on the independents to stop messing around with this, to stop playing politics with this,'' she told reporters in Canberra.

The lower house has now adjourned for the week and will sit again next Monday.

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