The Australian Department of Defence said the infiltrator “overwhelmed a duty member onboard a patrol boat” which was moored at HMAS Coonawarra, a naval base in the northern city of Darwin.
In a statement, it said: “The intruder overpowered the duty member, accessed the vessel’s armoury and removed a number of weapons.
“The person then departed the vessel with the weapons.”
The Australian newspaper said an Armidale-class patrol boat would be expected to carry a stock of machine guns, assault rifles, shotguns, 9mm pistols and ammunition in its armoury.
The attack happened on the Larrakeyah Naval Base which is now in lock-down. It was unclear whether the intruder accessed the boat from land or sea and the types of weapons taken have not been revealed.
Vice Admiral Ray Griggs told the Australian Broadcasting Association the intruder was “armed”, adding that the young sailor who was on guard is safe but very shaken by the incident.
He said: “Clearly his life was threatened, he is quite shaken but otherwise okay.”
Earlier reports suggested the sailor had been tied up.
The incident is being investigated by Northern Territory police and Australian Federal Police in conjunction with defence personnel.
Tropical Darwin is a key defence hub for Australia, with US Marines based in a barracks outside the city since April this year as Washington looks to deepen its presence in Asia.
Almost 600 Navy personnel are based in the area.