In a Tuesday evening estimates hearing, Attorney-General's Department deputy secretary Sarah Chidgey revealed the multi-million dollar cost only represented the case's external legal fees following former attorney-general Christian Porter's green-lighting of proceedings in 2018.
Mr Collaery is awaiting trial after pleading not guilty to five charges alleging he, and Witness K, breached national security information laws.
He is accused of sharing classified information about a 2004 operation in which Australian spies bugged a government building in East Timor to gain advantage during negotiations over lucrative oil and gas reserves.
Senator Patrick said the federal government had continued to suppress other critical information by disallowing, or failing to prioritise, relevant cabinet documents due for release at the start of the year.
He was concerned the ongoing situation had pushed East Timor to look more favourably toward China rather than Australia.
"After decades of controversy, revelations of Australian spying and highly secret criminal trials, it's high time that the whole story is revealed so that Australian-Timorese relations can move forward on a new basis of trust and transparency," he told The Canberra Times on Wednesday.
"The suppressed 2001 cabinet submissions and decisions are a key part of the history of a disgraceful episode in Australia's diplomacy, a story that continues to this day with the prosecution of Bernard Collaery.
"These cabinet papers should not be left in the government's black hole of shameful secrets."
Out of the 420 documents requested for the year, 223 had been released, 14 had been released with redactions while 135 were still awaiting assessment.
There were 49 documents entirely exempt from public release, according to the senator's analysis.
Senator Patrick suggested on face value it could appear that public servants were self-censoring based on "political winds".
He later told The Canberra Times it was important the archives agency prioritise the 2001 documents that remained of particular relevance.
"Many of these cabinet papers deal with subjects like climate change and refugee policy that are of great interest and importance today," he said on Wednesday.
"The archives' reluctance to release this material looks a lot like browbeaten bureaucrats trimming their sails to the sensitivities of their current political masters."
Assistant Attorney-General Amanda Stoker strongly rejected the South Australian senator's suggestion on Tuesday evening, adding it was a "baseless" insult to the apolitical bureaucrats who undertake the work.
"I'm not going to pretend that public servants don't at times make incorrect decisions. That's why we have tribunals. That's why we have appeal process," Senator Stoker said in response.
"But overwhelmingly, this is an agency that's about making information available rather than hiding it.
"To suggest that there's any kind of political motive is baseless, quite frankly.
"It's insulting to the hard work of the officers at the archives and it certainly does not reflect any instruction that has come from government."
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