The Beretta 92FS is handled by Council agents operating on foot as their main sidearm. This anachronistic since the original movie is set in the 1960s and this movie takes place in the 70s while the Beretta 92FS entered production in 1984.
Colt M1911
The Colt M1911 is seen in the hands of US Air Force personnel as their standard weapon since the movie is set in the 1970s.
Revolvers
Colt Single Action Army
A Colt Single Action Army was among the possessions of General Howard R. McKee (Larry Lamb) in his Yokota Air Base residence. He uses it to shoot Luke after he takes down Frank with an injection on his neck, but fails.
Nambu Model 60
A Nambu Model 60 is seen near the end of the film in the holster of a Tokyo Metropolitan Police Department officer (Huang Yonggang).
Assault Rifles
Colt M16A1
The Colt M16A1 is seen throughout the movie in the hands of US Air Force airmen.
Custom M16 DMR
A Council agent uses an M16 DMR customized for sniping work in order to assassinate Alice McKee in Shinagawa. It has a DPMS Hi-Rider upper receiver as identified by its lack of forward assist or brass deflector, rounded ejection port and raised Picatinny rail.
Auto Cannons
DEFA cannon
The DEFA cannon is the standard gun armament of the IAI Daggers standing in for the F-104 Starfighters stationed at Yokota Air Base in Tokyo's Fussa City. The IAI Dagger is an Israeli-built copy of the Dassault Mirage 5.
Colt Mk 12
The early model A-4 Skyhawks in the background are armed with Colt Mk 12 20mm cannons. The Colt Mk 12 was the US Navy's primary aircraft armament for much of the 1950's and 60's before the Navy went with the Air Force's M61 Vulcan.
Others
Cleaner Gun
The Cleaner Gun is used by Council operatives assigned to cleaning duty by wiping out chiropteran corpses in order to prevent public panic and show the world of their existence. Frank steals one from the two Council agents detained temporarily at Yokota Air Base. The cleaner guns work by melting off anything the mist comes into contact with.