A flare gun is a specialized gun designed to shoot flares. They are used solely for sending signals, mostly distress signals, for people out at sea or to aircraft from the ground. As such, it is not intended to be used as a weapon.
Militaires Sans Frontières
Although the private military group Militaires Sans Frontières didn't actually use flare guns themselves during the Peace Walker Incident in 1974, one of their weapons, the Kampfpistole, was modified from a flare gun.
On December 7, 1974, the MSF Intel Team agent Hideo utilized a flare gun to signal MSF's Hind chopper to his location when requesting an extraction, after his initial attempt at hailing them with an SOS transmission failed due to static interference.
Behind the scenes
Flare guns were first used as a "weapon" in the non-canon sequel to Metal Gear, Snake's Revenge, where it could be used to see in dark places. In addition, the enemy was also implied to use flares to aid in their searches within the jungle level.
Although flare guns have not been used canonically until Metal Gear Solid V: Ground Zeroes, and even then only in one of the Side Ops, one of the weapons in Metal Gear Solid: Peace Walker, the Kampfpistole, was based on a modified flare gun used by the Nazis during World War II.