In late 2009, senior US Navy officials raised concerns about security at Australian naval bases, querying whether American ships could dock safely.

A small number of serving defence personnel belong to outlaw bikie groups.

A company tied to an alleged crime boss was given contracts to guard sensitive naval facilities in 2006.

Plain-clothes undercover defence officials talked their way past security posts at half a dozen bases and on one occasion used a library ID card to enter a defence facility.

Naval personnel smuggled guns into Australia from south-east Asia in 2008 by stashing them in the storage cavity of an Armidale-class patrol boat.

A Defence Department document, obtained by the Herald, reveals that a review of the vulnerability of defence bases, ships and other assets called for a ground-up overhaul.

''A cornerstone recommendation [of the review] was a need to make significant changes to our training and execution model from the bottom up,'' the October 2009 document says.

The finding was made eight weeks after the Chief of the Defence Force, Air Chief Marshal Angus Houston, said he was confident ''the security arrangements in place at our bases are effective''.

While recent media reports have focused on fears about base security after police uncovered a terrorist plot to attack Holsworthy Barracks in 2009, law enforcement agencies have documented concerns about organised crime penetrating defence facilities for more than a decade.

In 2000, the Victoria Police drug squad created an intelligence file alleging that a group of navy personnel was importing cocaine through Garden Island naval base in Sydney.

In 2006, two state police agencies discovered that Global Protective Services, a company subcontracted to guard HMAS Penguin and Garden Island naval base, was linked closely to the Finks outlaw motorcycle gang member and organised crime figure Yassar Bakir. GPS is now deregistered and not associated with any business with a similar name.

Queensland police suspected that the now-jailed Bakir was simultaneously using GPS - whose naval base contracts expired in mid-2006 - to run drugs down the east coast. In 2005, another company linked to Bakir, Global Protection Group, also not linked to any business operating now, had a contract to guard the Randwick barracks.

Defence sources said the department was not only failing adequately to vet civilian subcontractors but had failed to detect or act on links between at least two dozen serving personnel and bikie gangs.

Police sources have confirmed strong associations between some defence employees and the Hells Angels, Rebels, Bros and Gypsy Jokers gangs, whose members include organised crime figures.

A police report seen by the Herald says a small number of military personnel are members of hardcore, outlaw bikie groups and have been implicated in ''weapons and drug trafficking''.

Meanwhile, NSW Police are investigating allegations that naval personnel at Garden Island are involved in a small drug-trafficking ring.

During the past two years, the threat posed by criminals or terrorists to defence bases has prompted the navy to form a force protection working group.

But the Herald has learnt that two lieutenants working with the group quit the navy in December because the group's recommendations were repeatedly stalled and ignored.

The revelations come after Defence told a parliamentary inquiry it was virtually powerless to search the tens of thousands of people who passed through the gates of its bases every day.

The right to search private is dependent on the contract signed between Defence and the company.