The man, dressed in military clothing and wearing a balaclava, allegedly overpowered a crewman on the Armidale class patrol boat HMAS Bathurst at the naval base Coonawarra naval base in the Northern Territory.
At around 1 a.m. Thursday a sailor aboard the ship was attacked and tied with plastic cable ties. The sailor, who suffered minor injuries, managed to escape and raise an alarm.
The military locked down the base and searched all vehicles entering and leaving.
Detectives for the police's Major and Serious Crime Squad on Saturday arrested a man, 40, at a Darwin city apartment and recovered a dozen semi-automatic pistols and two pump-action shotguns taken from the ship's armory, a report by ABC Australia said.
No ammunition is believed to have been stolen.
Northern Territory Police Commander Richard Bryson said police don't know what role the arrested man allegedly played in the armed robbery.
"Police are still trying to establish at this point in time whether or not this person has received the weapons shortly after the commission ... or in fact [he is] one of the principal offenders," Bryson said.
"Those are the matters yet to be established by the investigators."
The person who broke in appeared to have good knowledge of the layout of the patrol boat and military procedures around the base.
Bryson also said it appears several people were involved in the raid.
"Investigators will continue those investigations until all persons that had a hand in that conspiracy have been brought to justice," ABC quoted Bryson as saying.
Chief of Navy Vice Adm. Ray Griggs ordered an investigation into security on all Australian naval ships and bases.
Unnamed defense sources told the Northern Territory News that security at Coonawarra wasn't as stringent as that enforced at naval bases in Sydney and Melbourne.
Opposition defense spokesman Sen. David Johnston said the security breach was because the government canceled a $230 million military security systems upgrade program.
He said the breach was the second major security issue involving military bases after the a terrorist plot to attack Holsworthy Barracks, an army base in Sydney.
In August 2009 police arrested four men allegedly connected with the Somali terrorist group al-Shabaab charged them in conjunction with the suspected plot on Holsworthy Barracks.
In December last year a judge sentenced three Somali men, who had entered Australia as refugees, to 15 years each in prison for planning the attack.
A fourth man charged in connection with the case was acquitted because he had been trying to stop any act of terrorism, a report by the Herald Sun newspaper said at the time.