Four people who launched the action against the vaccination mandate, that ends on Wednesday, want taxpayers to settle their legal bill after withdrawing their case.

Lawyer for the group, Danial Kelly, said the government passed an amendment in parliament to retrospectively validate chief health officer Hugh Heggie's health direction.

He said the tweak made on May 19 "explicitly and only targeted the plaintiff's challenge to the validity of the chief health officer's directions regarding mandatory vaccination".

"The passing of the amendment ... suggests clearly that the defendant saw the strength of the plaintiff's case and that the action had reasonable prospects of success and was almost certain to succeed," he told the Supreme Court in Darwin.

Mr Kelly alleged that the government concealed its actions, which were made less than four weeks before the trial was due to start.

He said the government "perversely encouraged the plaintiffs to continue their legal challenge by knowingly concealing their knowledge that it was to become futile by the forthcoming amendment". He said the court should consider it misconduct and order it to pay costs.

"There has been something that is unreasonable and improper that has occurred."

Marii Oblelscuk, Ray Phillips, Conan Hammet and John Anstess launched the action challenging the health order requiring most workers to be fully vaccinated as the virus spread through the territory in December during the second wave of the disease.

The group claimed they were attempting to save their jobs and Dr Heggie didn't have the legal power to make the far-reaching directive.

"The plaintiffs lost their livelihoods through loss of income and business, at least one Aboriginal plaintiff, Mr Anstess, lost his ability to continue coaching his Aboriginal children in club sports," Mr Kelly said.

High-profile barrister and civil liberties advocate Julian Burnside was set to argue their case on 20 grounds, with evidence from medical expert Professor Nikolai Petrovsky from Flinders University.

The case was discontinued on May 30.

NT solicitor-general Nikolai Christrup SC denied the government had acted unreasonably, saying the court cannot and should not attempt to determine the outcome of the trial.

He called for the parties to pay their own costs.

"The suggestion the territory all along intended to pass legislation but deliberately kept this back from the plaintiffs not only finds no support in the evidence, it is in fact contradicted by it," he said.

Mr Christrup labelled it a serious allegation and asked: "What would the defendants have to gain by adopting such an outrageous position?"

"The answer is absolutely nothing. If that was the intention, why not tell the plaintiff about that in December (when the case was filed) ... There would be no downside."

Justice Sonia Brownhill replied to the rhetorical question saying: "In fact there would be an upside because the defendant avoids unnecessary legal work."

She reserved her decision and called on the parties to make further written submissions on the parliamentary process that led to the amendments passing into law and the impact on the costs application.

The matter was adjourned to a date still to be fixed.

Australian Associated Press