A CONTROVERSIAL super trawler will be banned from fishing in Australian waters for at least two years after federal government legislation passed the lower house.

The bill will prevent the 142m Abel Tasman, formerly known as the Margiris, from fishing for its 18,000 tonne quota in seas stretching from southern Queensland to Western Australia.

The Environment Protection and Biodiversity Conversation Amendment (Declared Fishing Activities) Bill 2012 was passed with the support of key independent MPs Craig Thomson, Andrew Wilkie and - at the 11th hour - independent MP Rob Oakeshott.

Oakeshott said until today, he had been planning to vote against the government's bill as he saw no reason to question the science on super trawlers provided by the Australian Fisheries Management Authority (AFMA).

But he changed his mind after Mr Burke told parliament some "serious'' questions had been raised since AFMA had told the government of new legal advice that it had not been correctly implementing some aspects of the Fisheries Act.

"For me, that was a significant response from the minister that there was some problems with those processes,'' he told parliament, to cries from the coalition.

"I accept the advice and the position of the government that they are raising doubts around how quotas are formed and how the science around that process is formed.''

He said another factor was that the government had finally provided the terms of reference for its root and branch review of the Fisheries Act.

Environment Minister Tony Burke moved several amendments to appease crossbench and coalition concerns about the reach of the bill.

Existing fishing operations and recreational fishing won't be caught up in the new laws, which will only cover environmental concerns, not social and economic ones.

At the request of Mr Rob Oakeshott, new bans cannot be made after 12 months from the bill taking effect, giving time for a promised review of fisheries management to take place.

Mr Burke earlier this week introduced legislation to temporarily ban the super trawler Abel Tasman from fishing in Australian waters, arguing it was better to err on the side of caution until further scientific studies were carried out.

AFMA recently stated it had found "no evidence'' that larger fishing boats like the Abel Tasman posed a higher risk to the marine environment.

Mr Burke, who represents fisheries minister Senator Joe Ludwig in the lower house, said he asked AFMA what impact the trawler could have on some fish species in the catch area.

"The answer was, we don't have that scientific information, and that was giving a green light to the vessel,'' he said.

The minister also said AFMA had informed the government in the past 24 hours of new legal advice that the authority had not been correctly implementing some aspects of the fisheries act.

Mr Burke said that raised some "serious questions''.

Mr Ludwig announced earlier this week a "root and branch'' review of the 20-year-old act.