A submariner turned senator has warned of significant cost blowouts in Australia's Future Submarine.

Defence says two planning documents due last year are still not finalised, but insists that there have been “no delays to key milestones” and no “cost or schedule impacts” in the $50 billion project.

But Senator Rex Patrick, a former Royal Australian Navy submariner, says military insiders have told him that the submarine program is “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 told the ABC.

The senator said the senior naval officer currently running the program should be replaced by a professional project manager.

“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.”

The Defence Department has strongly rejected the warnings.

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

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

“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”, the department said.

Questions have been asked about questioned the Senator's motivation for attacking the program, given that the South Australian had previously argued for German shipbuilder TKMS to be awarded the lucrative contract, and once 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.”