Japanese people believed the ninja had some supernatural powers such as controlling others’ minds or walking on the river. This is perhaps because people in the Iga and Koka regions had long been practicing hypnosis and botanics that arrived from China in the 6th century when Buddhism was introduced to Japan.
Prince Shotoku (574 ~ 622) reportedly had a famous spy named Otomono Sahito who is considered to be the fist ninja in history.
Despite the fact that the Iga and Koka towns are very close to Nara and Kyoto, the residents were not ruled by any samurai clan and commonly practiced shuugendo (esoteric Buddhism that promoted mountain training).
During the Nara period (710~794) the yamabushi (black-cap wearing mountain monks) emerged. They abstained from pleasurable things, maintained simple lives in the mountains and they were good fighters.
When the Tang Dynasty in China fell in 907, many monks and generals fled to central Japan. They shared their knowledge of warfare and Eastern philosophy mostly in the areas near Iga and Koka.
In 1162, a samurai from the Genji clan moved to Iga after losing a battle against the Taira clan and renounced his samurai status. He changed his name to Daisuke Tokagure. He later met with Kain Doshi, a monk who was exiled from China. Together they developed Tokagure-ryu, the first organized practice of guerrilla fighting and stealth techniques. These techniques are also called ninpo-taijitsu.
Historical records indicate the existence of shinobi during the Muromachi Period. There are references to ninjas who secretly burned the Hachimanyama castle and infiltrated the Ototsu Castle during the Nanbukochu wars (1336~1392).
During the Sengoku period (1477~1615) everyone was aware of the guerrilla fighters in Iga and Koka who maintained a communal life different from other towns in feudal Japan. Oda Nobunaga’s son tried to invade the town of Iga in 1579 but got defeated badly.
In 1581, Oda Nobunaga attacked the town again with the army of 40,000 men, The ninja were vastly outnumbered and lost against the army. Oda Nobunaga reportedly killed most of the Ninja back then.
It is said that Hattori Hanzo saved the life of Tokugawa Ieyasu in two occasions and was given the task of guarding the Shogunate in Tokyo. The district known as Hanzo-mon in Tokyo refers to the gate protected by Hanzo’s men.
During the Edo period (1603 ~ 1868) the need for ninja gradually decreased because of the peaceful political environment and the Kogi-Onmitsu, 3000 strong intelligence agents working for the shogunate.
Today there are dozens of tokagure-ryu ninpo and ninjutsu dojos in and outside of Japan. The leader of tokagure-ryu of Japan is Masaaki Hatsumi who is in his late 70s and the name of his organization is Bujinkan.