A Labor-led parliamentary committee in March agreed to shelve the major projects report into Defence, which has been prepared by the Australian National Audit Office since 2008.
The Joint Committee of Public Accounts and Audit previously said it would transition to a process where it "examines in greater detail the auditor general's performance audits in the Defence portfolio".
The decision was slammed as a blow to transparency and accountability for multibillion-dollar military projects.
But in the Senate on Wednesday afternoon, a crossbench motion requesting the auditor-general urgently reinstate the annual major projects report was passed.
Labor did not oppose the motion and the Australian National Audit Office is expected to provide a response to the request.
Dumping the major projects report was suggested by the ANAO, which told the committee it lacked the resources and found Defence increasingly non-compliant.
Greens defence spokesman David Shoebridge said previous audits found a collective 35 years of delay and $40 billion worth of cost blowouts across 21 projects.
"The Albanese government has overseen a staggering increase in Defence secrecy," he said.
"Meanwhile they squander billions in wasteful, overpriced and under performing procurement deals."
Concerns have been raised that a new Parliamentary Joint Committee on Defence will be used to evade scrutiny and allow poor performance to go unchecked.
Some senior government ministers were not informed about the decision to scrap the audit beforehand, AAP was told.
Defence Industry Minister Pat Conroy said he has always supported as much transparency as possible, particularly in relation to defence projects.
"I welcome the fact this motion was passed and would like to see the major projects report continue," he said.
"Ultimately, that's a matter for the committee."
Defence Minister Richard Marles said there were issues surrounding information being supplied in the current environment.Â
"We need to take that into account in terms of our national security," he told reporters in Canberra on Thursday.
"We want to be as transparent as we can be, and that's what our record has shown in defence, and in fact, across the government."
Opposition defence spokesman James Paterson said it was the worst time to be undermining the scrutiny of major Defence projects.
"The Albanese government should stop hiding behind hollow excuses and vague language and immediately instruct Defence to restore co-operation with the ANAO," he said.
"Richard Marles' excuses for the Albanese government's blatant disregard for transparency are frankly unconvincing."
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