Five projects are now also facing challenges living up to what was promised, including the $16.5 billion Joint Strike Fighter program.

The Australian National Audit Office's 2018-19 Defence Major Projects Report revealed the cost of the Defence Department's 26 major projects had reached $64.1 billion, compared to $39.7 billion when they were approved.

That means there's been a blowout of nearly $25 billion.

Projects were an average of 2.7 years behind schedule, or a cumulative 57 years.

While the situation had improved on the previous year, when projects were running 67 years late, the audit office said delivering major projects on schedule "continues to present challenges for Defence".

The projects with the greatest lag are the Collins R&S class of submarine, running more than nine years behind, and the MRH90 helicopter project, which is now more than seven years late.

The $3.77 billion helicopter program has been listed as a project of concern since 2011, which means it has received a higher level of oversight and management and undertaken more detailed reporting to government.

The program stopped accepting aircraft twice between 2011 and 2012 over technical and reliability issues.

The Chief of Army delayed the introduction of MRH90 into the 6th Aviation Regiment by three years, because of reliability and design shortfalls, while aircraft had to be retrofitted to bring them up to contracted standard.

However the aircraft still do not meet all of Defence's requirements.

The MRH90 program was still working with industry to contract, redesign and deliver outstanding requirements, including the Taipan gun mount, common mission management system, and new mission troop seats.

The Hawkei armoured vehicles project may also fall short of its promised capabilities.

The $1.98 billion program has missed milestones after engine manufacturer, Steyr Motors, entered voluntary administration.

The project is expected to complete its production reliability acceptance test 21 months later than originally contracted, while it may not fully meet the user's expectations due to scope, budget and vehicle design constraints, the audit warned.

The Joint Strike Fighter project is also under threat, due to g issues arising from internal cost growth, forecasting accuracy and external budget constraints.

Project capability may be affected as a result, the audit said.

The shortfalls have prompted Labor's defence spokesman Pat Conroy, and deputy chair of the Public Accounts Committee Julian Hill to call for a public inquiry into the Coalition government's management of defence projects.

"This mismanagement has the potential to have a real impact on the ground for the ADF and for Australian taxpayers," they said.

"The report raises serious questions about the delivery of key projects, including budget, capability and schedule performance. The project delays mean our troops are not getting the equipment they need, forcing them to use increasingly outdated weapons, ships and planes that are costing more and more to maintain."