It is believed the man did not conduct the brazen robbery, but was looking after the weapons after the late-night theft on Thursday.

Police suspect those behind the robbery may have naval links, and say they expect to make more arrests.

On Saturday police raided the man's inner-city apartment, where they recovered the weapons. Police said he tried to run away but was caught.

The man's arrest followed a robbery at a navy patrol boat moored at HMAS Coonawarra on Thursday night, in which a dozen semi-automatic pistols and two pump-action shotguns were stolen.

During the attack, a man wearing military attire and a balaclava overpowered and tied up a young sailor with cable ties. The sailor was unhurt.

Police Commander Richard Bryson said police believed several people were involved in the attack.

''The 40-year-old man has today been formally charged with one count of receiving stolen property, two counts of possessing a prohibited firearm and 12 counts of possessing a firearm without a licence,'' Commander Bryson said.

''Investigations are continuing into how the 40-year-old alleged offender came into possession of the stolen weapons.

''Investigations will continue until all persons that had a hand in that conspiracy have been brought to justice.''

He said police believed the offender knew the layout of the patrol boat, and the investigation would also consider links between the suspects and the naval base.

Navy chief Vice Admiral Ray Griggs has ordered a security review of all naval bases.