Lawyers fighting a two-year ban on a super trawler operating in Australian waters have been warned by a Federal Court judge to cast their nets with care when making allegations against federal Environment Minister Tony Burke.

Seafish Tasmania is asking the Federal Court to overturn a ban imposed by Mr Burke on the super-trawler Abel Tasman, while an expert panel considers the ship's possible impact on the environment.

In documents previously lodged with the court the company claimed the minister was advised that the impacts were known and any risks could be managed.

Seafish alleges Mr Burke was keen to ban the vessel and was searching for some power to justify his actions.

In his opening statement on Friday, Justice John Logan warned the company's lawyers their statement of claim risked breaking the Parliamentary Privilege Act, which emanates from the centuries-old Bill Of Rights.

Under the act, questions cannot be asked of ministers in court about their behaviour in parliament.

"Your statement of claim is scandalous, is it not, in asking this court to do what has been forbidden since 1689?" Justice Logan said.

Justice Logan suggested he may strike out sections of the claim.

"Such is the constitutional importance of the separation of powers between the state and the law," he said.

Justice Logan also warned that any allegation of the minister acting in bad faith was a "very particular and serious allegation to make".

He cautioned Mr Derrington of the consequences if he were to find such a complaint had no basis.

"I would be duty-bound to serve papers to the Bar Association," he said.

Roger Derrington SC told the court he had no intention of questioning what the minister said in parliament and did not call into question the minister's motivation.

He asked for leave to make amendments to the statement of claim.

"That would be a very prudent course," Justice Logan replied.

Mr Derrington said he would review both issues and particularise or remove them.

Any issues such as bad faith would be jettisoned in face of extending the trial in any case, he said.

The case has been set down for a three-day trial from June 25.


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