The Federal Court has upheld a ban on a controversial super trawler operating in Australian waters.

Seafish Tasmania had asked the Federal Court to overturn a 2012 decision banning a controversial super trawler from fishing.

The company brought a trawler to Australia in 2012 to fish an 18,000 tonne quota of mackerel and red bait.

After a public outcry by green groups, Federal Parliament passed legislation imposing a two-year ban, while an expert panel considered the environmental impacts.

In a judgment released today, Federal Court Justice John Logan found the ban by then federal environment minister Tony Burke was reasonable.

Justice Logan said the redress for the Government's actions was not to be found within the courts, but perhaps by people assessing the risk of investing in Australia.

Rebecca Hubbard from Environment Tasmania welcomed the court's decision.

"Today's decision is the right one, it obviously supports the environment and the fisheries ministers and the Government in doing what's necessary to protect our environment and our fisheries," she said.