Ninjutsu did not come into being as a well defined martial system and it took several hundred years of development and change to arrive at the historical system we know today, an established independent system of knowledge in its own right.
In 637AD, a warrior monk, En no Gyoja set up a Tendai Shugendo dojo in the Togakure Mountains of Japan: a place of ascetic learning and enlightenment. In 1181 Heike troops persecuted the area populace and crushed the dojo. Survivors fled to the SE regions of Japan to Iga province including one Daisuke Nishina who was born into the sect in 1165. For his rebirth he took his village name and became Daisuke Togakure, thus the Togakure Ryu was born. Eventually there were over 200 Ninja families in Japan and the height of their activity was between the 13th and 16th centuries.
With the start of the Meiji period in 1868 peace was restored to Japan and all martial arts were considered barbaric and stripped of their warrior significance, with many becoming “do” arts. Ninjutsu went underground and only resurfaced with the death of Soke Takamatsu in 1972. His wish was that Ninjutsu should be available to the rest of the world and in 1975 two westerners brought Ninjutsu out of Japan after training with Soke Hatsumi and receiving his blessing to teach the art.
Soke, Hatsumi now runs the global BUJINKAN organisation from his Dojo in Noda City, Chiba Prefecture in Japan. The Bujinkan comprises of 9 schools or Ryu, some of which are Ninjutsu schools and some Samurai schools. 33rd Soke Takamatsu inherited these schools and passed these on to Hatsumi Soke upon his death in 1972.
34th Soke, Dr Masaaki Hatsumi is regarded as the last living ninja master with lineage dating back nearly 1000 years. He is also regarded by the Japanese government as a “living treasure”.
Note: This is only a broad-based overview of Ninjutsu’s history.