CP Snow once said that all ancient British traditions date to the second half of the 19th Century, and his only error was to limit this claim to Britain. The great majority of real traditions having been swept away or reduced to irrelevance with the rise of capitalism, the 19th century saw the rise of a whole set of new ones, which were then fixed in shape by the system of nation-states, each with their own newly-codified language and officially sanctioned history that took shape at the same time. – John Quiggan
There are basically no publications in English on ninja worth reading–it’s all junk. The only serious academic scholarship available outside Japanese language publications would be the material on Roy Ron’s website at ninpo.org. Roy is a (fairly) recent PhD graduate from U Hawaii, and has spent a number of years doing research on ninja and related topics.
The most reliable reconstructions of "ninja" history suggest that "ninja" denotes a function, not a special kind of warrior--ninja WERE samurai (a term, which didn't designate a class until the Tokugawa period--AFTER the warfare of the late medieval period had ended--before that it designated only an occupation) performing "ninja" work.
Movie-style ninja, BTW, have a much longer history than the movies (although the term "ninja" does not appear to have been popularized until the 20th century). Ninja shows, ninja houses (sort of like American "haunted houses" at carnivals), and ninja novels and stories were popular by the middle of the Tokugawa period. The "ninja" performers may have created the genre completely out of whole cloth, or they may have built on genuine lore derived from old spymasters. Either way, however, it's clear that much of the lore underlying both modern ninja movies and modern ninja schools has both a long history AND little basis in reality outside the theatre.
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Another problem stems from the nature of Japanese society and Japan's social history. From the early seventeenth century until the middle of the nineteenth century (Meiji Restoration) Japanese society was locked in a rigid class structure that allowed very little or no mobility at all. That meant that members of a social group within a certain social class had no choice but to accept their place in society. In addition, there was a clear distinction between the ruling class--the samurai--and the other classes--peasants, craftsmen, and merchants. Within each class as well, there was a certain hierarchy according to which members of the class had to act their social role with little opportunity to change their status. This reality have produced strong identifying characteristics for each social class to which the individual had to conform. Outside these social classes, as they were designated by the ruling samurai elite, were the classless people and outcasts who were placed bellow everybody else. Ninjutsu, for the most part, was the fighting skills and methods practiced by a small number of families who belonged to the lower samurai class, peasants, and even outcasts, and only rarely by warriors belonging to the samurai elite. Consequently, ninjutsu since the Edo period has been identified as different than the noble traditions of the samurai, and those practicing it were usually regarded by the rest of society as lowly people. In other words, ninjutsu was anything but conformity to the pre defined social rules. As such, it could have never received a seal of approval as a recognized martial tradition, not even when those samurai were actually employing warriors proficient in ninjutsu.
The social conditions and the strong tendency for conformity I have just discussed produced another problem. Fighting methods or weapons that were not practiced by the samurai elite were considered mysterious at best, sometimes demonic, often super natural, and certainly unworthy of respect. Here again is the problem that rises from social conformity. For the samurai elite who were bound by rules of behavior and a code of honor and ethics, fighting methods were confined to a small number of weapons, namely bow, sword, staff, jutte, and spear. This resulted in little creativity in fighting. However, for warriors other than the samurai, those who were not constrained by their position in society, creativity was a necessity for winning. They have maintained unusual and innovative fighting methods and weapons that were developed in earlier periods, while systematizing, recording, and adding to it during the Edo period. Consequently, ninjutsu came to be perceived very negatively, and when Japan moved into the modern period ninjutsu gradually disappeared while its dark and mysterious image, which already became folklore, was now viewed as an historical fact.
And yet, in the 1921 Ryūkyū Kenpō: Karate, the first fully published karate text, little of this [historical development of karate traditions] appears: karate is not a dō, lacks mythology, and is frank about recent Chinese influences. Reaching further back, to the unpublished writings of Itosu Anko, karate lacks even a name, makes no claims on the spirit, and mentions history not at all. Beyond that, the writing is in Chinese. Strangest of all, and most easily overlooked, is that through the 1920s there was only really one name: karate, the Chinese hand…
But the historical imperative was not a simple descriptive one, for it included certain strategic silences. They needed to know the details of their mystical origins, but they also needed to be at a loss to make a full accounting of the middle of karate history. Make no mistake: karate history soon had a middle, but it was indistinct—an outline with many precise gaps, a carefully composed picture of fog—because along with the questions that required answers were ones that could not be asked at all… --Craig Colbeck: Karate and Modernity, A Call for Comments
Bushidō, meaning "Way of the Warrior", is a Japanese code of conduct and a way of life, loosely analogous to the European concept of chivalry. It originates from the samurai moral code and stresses frugality, loyalty, martial arts mastery and honor unto death. Bushidō developed between the 9th to 12th centuries as set forth by numerous translated documents dating from the 12th to 16th centuries (as mentioned below). However, some dependable sources also state the document might have been formulated in the 17th century.
According to the Japanese dictionary Shogakukan Kokugo Daijiten, "Bushidō is defined as a unique philosophy (ronri) that spread through the warrior class from the Muromachi (chusei) period." Nitobe Inazō, in his book Bushidō: The Soul of Japan, described it in this way. "...Bushidō, then, is the code of moral principles which the samurai were required or instructed to observe... More frequently it is a code unuttered and unwritten... It was an organic growth of decades and centuries of military career."
Under the Tokugawa Shogunate during the Edo Period (1603-1867), Bushidō became formalized into Japanese Feudal Law. –Adapted from the Wikipedia