The cost of Australia's Future Submarine program is likely to blow out by billions of dollars because it is already missing key deadlines, a former defence contractor turned senator has warned.

Key points: Senator Rex Patrick says a professional project manager should be hired to oversee the program

Senator Rex Patrick says a professional project manager should be hired to oversee the program He says there could be a cost blowout of between $1 and $2 billion based on current evidence

He says there could be a cost blowout of between $1 and $2 billion based on current evidence The Defence Department says the work will be "within approved funding"

In December, Defence confirmed two planning documents due to be released last year had yet to be finalised, but the department insisted there had been "no delays to key milestones" and no "cost or schedule impacts" to the $50 billion project.

Senator Rex Patrick, who once also served as a Royal Australian Navy submariner, has not been convinced and said some military insiders were privately conceding the submarine program was "starting to go a little bit off the rails".

"Given that the project is running across three to four decades and is a $50 billion program, these sorts of delays, they cascade through — it could be a $1 to $2 billion blowout on the evidence that we have at the moment," Senator Patrick said.

Admiral running sub program has 'never run a minor project'

The South Australian politician, who took Nick Xenophon's seat in the Upper House last year, also suggested a professional project manager should replace the senior naval officer currently running the program.

"Rear Admiral [Gregory] Sammut is a highly respected and highly capable naval officer, however he's never run a major project, he's never run a minor project," Senator Patrick said.

"There are a number of highly qualified, highly experienced project managers in the mining industry, in the chemicals industry, in the IT industry that can be brought in to offer assistance for this extremely important program."

In a statement, the Defence Department strongly rejected Senator Patrick's warnings of cost blowouts and delays to the program being run with French company Naval Group.

"Requests for proposals have been issued to key equipment suppliers, and the procurement process is progressing to support subsequent design activities," the department said.

"The supporting work required to achieve key milestones continues to be managed ensuring those milestones are met on schedule."

The department added that "all work continues to be conducted within approved funding" including "the development of the Australian Industry Capability Strategy, which will be done by Naval Group".

Senator wanted German shipbuilder

Senior military sources have privately questioned the Senator's motivation for attacking the program, pointing out the South Australian had in the past argued German shipbuilder TKMS should have been awarded the lucrative contract.

Senator Patrick has rejected suggestions he was compromised by his past views or his decision to release leaked documents connected to Naval Group's Scorpene submarine contract with India.

"I have no issue with Naval Group being the selected submarine provider, they are a highly capable submarine design and build company," he said.

"However the program that they've been asked to execute, the program that's been selected by the Prime Minister, is a highly risky program, it's a new design of submarine."

Naval Group has declined to comment on Senator Patrick's comments.