Richard Boyle appeared in the civil jurisdiction of the South Australian District Court on Tuesday to challenge the legality of the allegations again him.

He will argue that his actions over releasing protected information were consistent with the Public Interest Disclosure Act and he is immune from prosecution.

Counsel for the Commonwealth and for Boyle initially asked Judge Liesl Kudelka to rule on the administration of a particular section of the act, but she refused without having the facts of the case before her.

"I'm very reluctant to make a decision about the law before all the evidence is before me," Judge Kudelka said.

"I'm here to decide the facts of this case and how the act, as you submit I need to interpret it, applies to those facts that I've found."

The judge said the parties could "absolutely have a crack" at preparing a set of agreed facts, but warned that they would need to be comprehensive if she was to proceed in the manner proposed.

"I'll wait to see how comprehensive or otherwise your facts are. But do not proceed on the basis that I'm necessarily going to accept that process," she said.

"I do not see that as the appropriate way of proceeding here."

In the criminal case, Boyle is facing 24 charges related to the release of protected information.

If his case makes it to trial it is not expected to go before a jury until 2023.

His civil action to block the prosecution is the first of its kind and will be instrumental in determining the strength and effectiveness of national whistleblower protections, which Attorney General, Mark Dreyfus, is considering reforming.

The Human Rights Law Centre has urged Mr Dreyfus to intervene and discontinue the prosecution of Boyle.

"Whistleblowers should be protected, not punished," Kieran Pender, a senior lawyer at the centre, said.

"Richard Boyle did the right thing - he spoke up about wrongdoing taking place within a powerful government agency."

Boyle first raised his concerns through internal ATO processes and then made a complaint to the tax ombudsman before taking part in a joint media investigation.

In those reports, he revealed ATO staff had been instructed to use harsher debt collection tactics on indebted individuals and small businesses.

Those tactics included the use of orders that require a bank to hand over money from a personal or business account without the permission of the taxpayer.

Follow-up reviews found Boyle's allegations of aggressive debt recovery practices at the ATO at the time were valid.

A federal parliamentary report also found the ATO had conducted a "superficial" investigation into his public interest disclosure.

Mr Pender said there was no public interest in Boyle's prosecution proceeding.

"Boyle has been vindicated by three independent inquiries, which collectively found that the ATO had misused its debt recovery powers, and that the ATO's internal investigation of Boyle's whistleblowing was superficial," he said.

A spokesman for Mr Dreyfus said the attorney-general did not comment on cases before the courts.

Mr Dreyfus previously said he hoped to update the Public Interest Disclosure Act next year to "reform and improve the scheme" protecting whistleblowers.

Boyle's civil proceedings will return to court on Wednesday.

Australian Associated Press