Darwin's naval base went into complete shutdown this morning after a breach of national security overnight, involving an assault on a sailor a theft of military weapons.

Northern Territory Police is investigating how the sailor was overpowered and tied up while weapons were stolen from a patrol boat at around 1am this morning.

Vice Admiral Ray Griggs said the "armed intruder" removed a cache of weapons from the armidale patrol boat, but would not say which type of weapoons they were.

"This is a very serious crime and something we're very concerned about and I don't want to say anything that would jeopardise the investigation," he told media.

He has ordered an immediate review of security at the base and on board the ships.

The young sailor who was assaulted and tied up is said to be safe but very shaken by the incident.

"Clearly his life was threatened, he's quite shaken but otherwise okay."

Major and serious crime detectives have been at the HMAS Coonawarra base in Larrakeyah, where all vehicles were being searched this morning.

"Major and Serious Crime Detectives are currently investigating in conjunction with Defence personnel and the AFP," Crime and Specialist Support Commander Richard Bryson said.

It is not known whether the intrusion came from the sea or land.

Police are appealing to the public for anyone with information to call the Police Assistance Line on 131 444 or Crime Stoppers on 1800 333 000.