Obtained by the ABC under Freedom of Information, the recent quarterly performance report from the Department of Defence's Capability and Sustainment Group, listed two major projects, the ADF's MRH90 helicopters and the Deployable Defence Air Traffic Management and Control System as areas of concern.

Although much of the detail has been redacted on "national security" grounds, the protected 86-page document marked "sensitive" confirms the projects remained on the concern list.

The report said Australia was spending $3.5 billion on 47 new MRH90s - a multi-role helicopter to be used by both navy and army, replacing the retired Sea King and ageing Black Hawk fleets.

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The utility helicopters undertake battlefield lift operations, support domestic counter terrorism operations and facilitate the expansion of the ADF's amphibious deployment and sustainment capability.

A number of MRH90s helicopters are embarked on various RAN ships, while the aircraft's home squadron is 808 at the Nowra based Fleet Air Arm station.

Defence sources acknowledged the MRH90's capability and sustainment has improved, but there are concerns over the delivery and service release of the enhance cargo hook system.

Defence rebuked claims in the ABC report that the aircraft also has issues with the auxiliary power unit on board, which limits the fleets' capability on certain missions because it cannot shut down its main engines due to problems with the power unit.

A defence spokesperson said that claim was "incorrect".

"The ABC report, which stated that, 'the fleet is currently limited because if the aircraft is flying a multi-stop mission, it cannot shut down the auxiliary power unit on board' is incorrect," the spokesperson said.

Key risks and emerging issues, mitigation strategies and risk ratings for the aircraft have all been removed from the report.

The report says delays to the program will have an impact on the sustainment of the existing helicopter fleet.

"There is a chance that the MRH program may not be able to retain sufficient levels of experienced and skilled workforce to achieve the required rate public acquisition deliveries leading to an impact on schedule and capability," the report said.

The Deployable Defence Air Traffic Management and Control System, is being purchased for use in possible conflict zones to prevent accidents between aircraft.

Another 14 purchases are identified on a less critical "projects of interest" list, including amphibious ships, new air combat capability and light protected mobility vehicles.

Australian Strategic Policy Institute senior fellow Andrew Davies told the ABC while defence generally appeared to have the cost of projects under control, the department was struggling to deliver capabilities on schedule.

He also believed the defence department was being unnecessarily secretive about its problems.

"Defence has been getting more and more secretive, or less transparent, year by year for the last decade or so," he said.