Australia's hopes of blocking a controversial super-trawler from fishing in its waters looked uncertain Wednesday with the opposition speaking out against the move and a key independent lawmaker expressing reservations.

Environment Minister Tony Burke has introduced legislation to prevent the Dutch-owned FV Margiris, recently reflagged as the Abel Tasman, from fishing in Australia until new scientific research into its impact can be carried out.

It follows a community backlash against the 9,500-tonne, 143-metre (469-foot) trawler led by fishermen and conservation groups concerned about over-fishing and bycatch of other creatures in its huge nets.

But the conservative Liberal/National opposition said it would not support the amendments to Australia's environmental protection and conservation laws, describing them as a "Trojan horse operation".

"(It) introduces a new level of ministerial power which is extraordinary, arbitrary and unfettered," said opposition environment spokesman Greg Hunt.

Burke said the opposition's position meant it was now "not clear whether the bill will pass parliament."

Centre-left Labor leads a minority government and will need the support of Greens MP Adam Bandt and a clutch of rural independent lawmakers to get the amendments through.

Bandt has already indicated his support along with independent Andrew Wilkie from the southern island state of Tasmania, where the Abel Tasman is set to fish.

Outspoken Queensland MP Bob Katter has been vocal in his opposition to the trawler but is yet to express a view on the amendments, as is fellow independent Tony Windsor.

Rob Oakeshott, the fourth unaligned MP on whom the government relies to pass legislation, said he was unlikely to support the move because it would undermine research by the independent Fisheries Management Authority (FMA).

"I have no reason (to believe) that over the last three years, their work on establishing a quota in preparation for a large vessel to work, (that) that quota has flaws in it," he said.

"It's an issue of science and actually believing in the processes of science."

The FMA has dismissed concerns about over-fishing, saying the trawler would be allowed to catch just 10 percent of available fish and would have little, if any, impact on the broader eco-system.