The department's senior submarine naval architect retired at the end of last month, taking 30 years of specialist experience with him, and a colleague has transferred to another area of the department, leaving just one public servant working in the safety-critical role.

The Defence Department said it had eight naval architects working on its submarine programs, but would not say if the specialists were Defence employees or contractors.

The specialist's union says the skill shortage has raised the risk to lives at sea to "an unacceptable level".

Naval architects perform a safety-crucial role, ensuring the stability and structural soundness of existing and proposed naval vessels from submarines to frigates and patrol boats.

The revelation comes after a difficult week for the future subs program, with the government forced to warn the French manufacturer of Australia's new generation of submarines over a cyber leak of sensitive information on subs being built for the Indian navy.

But the department is aware of the problem: the Royal Institution of Naval Architects warned in a 2015 submission that the department's naval architecture staffing level was in "functional disintegration" posing "significant risks" to Australia's defence capabilities.

Of the three submarine naval architects currently on staff at Defence, one retired on August 31 from his role on the Collins sustainment program and another has walked away from her job on the SEA1000, the $50 billion future subs project, moving to the Defence Science and Technology Group.

The move leaves just one in-house naval architect working in the Navy Technical Bureau.

In 1995 when Defence was both maintaining existing subs and the first Collins Class boat was hitting the water, there were around eight submarine naval architects.

The number had dwindled to five by 2005 when the specialists were engaged in maintaining the Collins boats but by 2015 there were just three naval architects shouldering responsibility for both the Collins and the Future Submarine program.

Dave Smith, of technical union Professionals Australia, was scathing of Defence's failure of succession planning for its specialist workforce.

"Navy civilian engineering has been a problem for a long time," Mr Smith said.

"The risk to lives, capability and cost is at an unacceptable level when you divest yourself of your internal expertise.

"The loss of the Kanimbla and Manoora supply ships at a cost of $500 million was connected to the running down of the Navy civilian engineering workforce and the inability to ensure contracted maintenance was being appropriately performed.

"This led to the Rizzo Review and a lot of rhetoric about rebuilding engineering capability.

"This rebuild has been stopped in its tracks by a mindless approach to reducing the APS workforce, with technical mastery residing in the levels most under attack, and a push to outsource and contract out as a first resort approach to staffing."

A Defence Department spokesman denied the subs program was short of expertise.

"Defence has no shortage of expertise," the spokesman said.

"The Department currently has eight naval architects dedicated to submarines, six within the Future Submarine Project and two within the Collins Program.

"Naval architecture work across the Department is performed by appropriately qualified and delegated professionals within the military engineer community, the Australian Public Service and industry suppliers, who operate under Defence's technical regulatory framework.

"Recruitment action is currently underway to engage more structural and mechanical engineers encompassing the skill set of naval architecture as we begin design work for the Future Submarine Program."