A Darwin navy base has been in lockdown after an armed intruder broke in, stealing a cache of weapons early on Friday morning.

At least two pump action shot guns and 12 semi-automatic pistols were stolen but no ammunition was taken from the armoury of a patrol boat moored at HMAS Coonawarra.

The intruder overpowered the duty officer on board the HMAS Bathhurst and tied him up, before stealing the cache.

On Friday, Northern Territory police locked down the base and searched all exiting vehicles but the weapons have not yet been found.