The Coalition government has spent more than $3 million prosecuting Bernard Collaery and Witness K, as officials reject claims the lawyer and whistleblower have been subjected to a secret trial.
Officials from the Attorney-General's department told Senate estimates as of October 6, the cost of the external legal advice as well as government solicitor costs in the case had reached $3,094,583.
That cost had risen by $600,000 in the past three months, according to independent Senator Rex Patrick.
"It just goes to the extraordinary cost to the taxpayer of this matter," Senator Patrick said.
Attorney-General's department secretary Chris Moraitis defended the extraordinary figure, saying there had been increasing discussions under the National Security Information Act.
"All trials cost," Mr Moraitis said.
Senator Patrick replied, "I'm just surprised at the rate of climb."
Mr Moraitis said, "Hopefully we can decelerate that rate."
Labor senator Kim Carr questioned why Attorney-General Christian Porter was yet to make a public statement outlining the rationale for the prosecution.
"This is a case where the government takes the view that an example has to be made of this individual isn't it?" Senator Carr asked.
Officials declined to comment.
Mr Moraitis also rejected suggestions Mr Collaery and Witness K were being prosecuted in secret.
"It's not a secret trial according to the National Security Information Act," he said.
"It balances the rights of national security matters and the rights of the defendants as well as it's up to the judge of the day to make a call on that after listening to the evidence introduced from both sides. That's what's happened in this case as far as I know."
"The court has been closed for certain hearings," Senator Patrick pointed out.
Mr Moraitis said that was the "nature" of the act.
"My understanding of the National Security Information Act is that the defendant or defendants are allowed to see the evidence, juries are certainly allowed to see the evidence, parts of hearings aren't made public but that's the nature of the material," Mr Moraitis said.
"That's not my definition of a secret trial."
Mr Collaery, a lawyer and former ACT attorney-general, is awaiting trial after pleading not guilty to five charges alleging he breached national security laws and conspired with former spy Witness K to do so.
He is accused of sharing protected information about an operation in which Australian spies bugged a government building in East Timor during negotiations over oil and gas reserves.
Mr Collaery's legal team is currently appealing a ruling that parts of his trial will be held in secret.
Mr Porter has issued a certificate to shield from the public evidence that he considered to be of national security importance.