The first occasion in which the presence of the "ninja" was widely reported was the "magari no jin (Battle of Magari, an old town in Shiga prefecture)" in first year of Chokyo period (1487). It was the conflict of Ashikaga Yoshinao, the 9th shogun of the Kamakura shogunate, who attempted to subjugate Sasaki Rokkaku (the ruler of the southern part of Shiga) who had disobeyed his orders. Throughout this conflict which lasted for about 3 years until Ashikaga Yoshinao died, the "Koga ninja" defended the clan of Sasaki, support that received nationwide approval.
They had to defend themselves against the armies in the west long enough for the Tokugawa army to regroup for the fight in Seki Ga Hara in the east. There were 400 Samurai from Koga Ryu who were called into action and aided with the defense of Fushimi Castle. Some of the ninja were in the castle, while the others terrorized and harrased the enemy outside with different kinds of raids. About 100 of the Koga ninja were killed in the battle.
One of the last times the Koga ninja were active in a battle was at Shima-Bara No Ran, when Christian samurais rebelled and occupied the Hara castle in Shimabara province on Kyushu. Ten ninjas from Koga Ryu were sent by Izumo Kami Nobutsuna to gather information for the Shogun’s samurais to prepare an attack against the castle.