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The Heckler & Koch P7M13 is the personal sidearm of Public Security Bureau officer Rei Furuya aka Black Organization Agent Bourbon.
IMI Jericho 941
The IMI Jericho 941 is the personal sidearm of FBI agent Shuichi Akai, who previously went undercover in the Black Organization.
M1911A1
A M1911A1 is seen in "Kyogoku Makoto the Understudy (Part One)" with a KEG48 stuntman filming an action scene.
Revolvers
Nambu Model 60
The Nambu Model 60 is seen with officers of the Tokyo Metropolitan Police.
Shotguns
12 Gauge Double Barreled Shotgun
An over and under-type 12 Gauge Double Barreled Shotgun is seen in "The Poodle and the Shotgun (Part 1)" and "The Poodle and the Shotgun (Part 2)". One is used in "The Skilled Hawk Hides His Crimes" by Genichi Takehara.
Sniper Rifles
Accuracy International Arctic Warfare
The Accuracy International Arctic Warfare is seen with Akai as his primary weapon.
Others
Crossbow
A crossbow is used by a murder suspect in "MPD Transportation Department (Part Three)", which was later used in a trip wire-type trap in "MPD Transportation Department (Part Four)". It's also used in a similar trap in "The 36-Cell Perfect Game (Part Two)".