Police have called the incident a breach of national security.
The ABC understands the break-in at the HMAS Coonawarra base, close to the Darwin central business district, happened about 1am.
It is believed a single intruder armed with a gun and wearing a balaclava boarded the Armidale-class patrol boat Bathurst, which was moored at the base.
A Northern Territory Police spokesman said a crewman on board was assaulted and tied up before the intruder broke into the boat's armoury.
He said two pump-action shotguns and a dozen 9mm pistols were taken.
An Armidale-class patrol boat would carry a stock of machine guns, assault rifles, shotguns, 9mm pistols and ammunition in its armoury.
Territory police Commander Richard Bryson says it appears the offender appeared to be familiar with the layout of the boat and ADF procedures.
He said a "cache" of weapons appeared to be missing.
He said it was believed no ammunition or magazines for the weapons had been taken.
Commander Richard Bryson of the Crime and Specialist Support Command says an investigation of the incident is being assisted by Australian Defence Force officers and the Australian Federal Police.
The naval base went into security lockdown, with vehicles being searched and contractors servicing the base turned away.
Authorities later began allowing restricted access to some personnel and contractors as police guarded the entrance to the base.
All patrol boat operations out of the base have been suspended, while all Navy personnel have been told to stand down and not return to work until Monday.
Navy chief Vice Admiral Ray Griggs says he has ordered an investigation of security on RAN ships and bases in light of the break-in.
He says the crew member whose life was threatened is being looked after and the security breach is being investigated.
"That is something that we need to obviously look into very carefully," he said.
"There is... an investigation underway from a police perspective, but I have also initiated a review of security on board our ships and establishments."
The Royal Australian Navy bases 10 of its 14 patrol boats in Darwin.
Federal Opposition Defence David Johnston says the break-in shows the Government was wrong to cut ADF spending.
He says $5.5 billion should not have been cut from the Defence budget, and the Opposition would restore the budget to between $28 billion and $30 billion.
"The sort of cuts that have been administered to Defence have to have some sort of effect over time," he said.
"One of them appears to be a reduction in security in terms in ingress and egress of the base up there in Darwin."
Security at the Darwin base is largely handled by civilian contractors.
Defence Minister Stephen Smith has declined to comment on the incident.