The Abbott government will fight in court to uphold a ban that prevents super trawlers fishing in Australian waters.

The federal court last month ruled against Seafish Tasmania, which was trying to overturn a two-year ban on super trawlers imposed by the previous Labor government.

Seafish Tasmania has lodged an application to appeal the decision, but Environment Minister Greg Hunt says the government will oppose it.

"The coalition government supports sustainable fisheries management and practices," he said in a statement.

Seafish Tasmania brought the factory freezer trawler Abel Tasman to Australia in 2012 to fish a 16,000-tonne quota of mackerel and redbait.

But that year it was banned by former federal environment minister Tony Burke for two years until its environmental impacts were assessed independently.

Prime Minister Tony Abbott recently told parliament the temporary ban on super trawler fishing in Australian waters would stay put.

The federal court has yet to appoint a date for the appeal hearing.