Meriki Onus and Crystal McKinnon are accused of breaching the Chief Health Officer's COVID-19 directions by arranging the protest in June 2020.

They were charged almost a year later and then notified on June 29 this year that charges would be dropped because they were "fatally flawed".

But prosecutors say the acting sergeant who made that call didn't have the authority to do so and the charges are continuing.

"There's no great conspiracy here about malfeasance, or a political decision," Andrew Sim told Melbourne Magistrates Court on Wednesday.

"It was an error about someone thinking they had the file and they didn't."

Barrister Felicity Gerry QC, representing the women, wanted police to hand over a series of documents that they believe may show the women have suffered an injustice, including that the legal system has been brought into disrepute.

Victoria Police boss Shane Patton challenged a subpoena through Mr Sim, who described the application as a fishing expedition.

It would require an oppressive exercise, searching individually through more than 50,000 documents for details that may not exist, he said.

Mr Sim said it was regrettable the women were notified of an intention to withdraw the charges, but noted it was just an intention.

Magistrate Andrew McKenna rejected the application in full on Wednesday afternoon.

He said the women's case seemed be that it was in the interests of justice that the early communication that the charges were being withdrawn should bind Victoria Police, and disable them from any future resurrection of the charge.

"When first addressed to me, this argument seemed a little exotic," he said.

"As a matter of law, no charge is in fact withdrawn until the court ... accepts the submission for withdrawal of a charge."

But Dr Gerry described the intended withdrawal, communicated to the women first and later confirmed by their solicitor, as unequivocal.

"One has to be able to rely on those processes when you have someone working in the Melbourne Prosecutions office, otherwise it's chaos," she said.

She made observations about Mr McKenna's body language during the hearing.

"I saw Your Honour roll your eyes," she commented at one point.

Later she told him she wasn't sure why he was shrugging.

Mr McKenna said sometimes decisions go through a number of hands, including some with different views, before a final result.

"These things happen. And with more regularity than perhaps some might appreciate," he said.

Australian Associated Press