Tasmanian Senator Richard Colbeck said the Federal Government would introduce regulations under the Fisheries Management Act to ban factory freezer vessels more than 130 metres in length.
A temporary ban on super trawlers was introduced in late 2012 to block the controversial FV Margiris, the world's second-largest trawler at the time.
That ban was set to expire in April 2015.
The Margiris, with its 300-metre long net, was capable of processing 250 tonnes of fish a day.
Seafish Tasmania had planned to use the 143-metre Dutch-owned vessel to net its 18,000 tonne quota of jack mackeral and red bait from an area stretching from Western Australia to Queensland, past Tasmania.
Supporters said the catch was sustainable and based on credible scientific research.
It's just not going to be enough to protect our protected species and our fisheries from the impact of these really large industrial trawlers - Rebecca Hubbard, Stop The Trawlers
Opponents argued the super trawler would deprive bluefin tuna of their natural prey and drive them out, with flow-on impacts for fishers and tourism.
A petition with 30,000 signatures was delivered to Canberra ahead of the temporary ban.
Senator Colbeck said the Government accepted many people in the community had legitimate concerns about the operation of super trawlers.
He said the decision "brings into force the Prime Minister's statement in March that super trawlers will remain banned".
Rebecca Hubbard from the Stop The Trawler campaign group said the new ban would do little to protect Australian fisheries, since many factory freezer trawlers were under 130 metres in length.
"That number is just not relevant; it's just not going to be enough to protect our protected species and our fisheries from the impact of these really large industrial trawlers," she said.
Ms Hubbard said the way in which a vessel can hunt and harvest fish was just as important, if not more important, than its length.
"It's more about that capacity to stick with fisheries, with schools of fish, and to keep taking, and to keep also impacting on protected species like seals and dolphins as well," she said.
Ms Hubbard said the terms of the ban needed to be more restrictive.