The Federal Government will go to trial in Brisbane to defend accusations it improperly banned a Dutch super trawler from operating in Australian waters.

Seafish Tasmania and Dutch-owned Pelagic want a two-year fishing ban overturned, along with a ban on working as a floating factory ship.

They are arguing that Federal Environment Minister Tony Burke sought to stop the ship despite advice the risks could be managed.

In the Federal Court in Brisbane today, Justice John Logan warned the barrister acting for the two fishing ventures that any unfounded allegation the Minister acted in bad faith would prompt a referral to the Bar Association.

He also said questioning parliamentary behaviour risked scandal and breaching the doctrine of the separation of powers.

The barrister agreed to make the necessary amendments.

The trial is due to begin in June.