According to Wikipedia, "By the time of the Meiji Restoration (1868), the tradition of the shinobi had become a topic of popular imagination and mystery in Japan. Ninja figured prominently in folklore and legend, and as a result it is often difficult to separate historical fact from myth. Some legendary abilities purported to be in the province of ninja training include invisibility, walking on water, and control over the natural elements. As a consequence, their perception in western popular culture in the 21th century is often based more on such legend and folklore than on the historical spies of the Sengoku (15th-17th Century) period."
I have completed 3 small "hit teams" that can be used in either the Bushito or Daredevil Adventures RPGs by Fantasy Games Unlimited. These were two of my favorite RPG Games. I ran a Daredevil's campaign and my good buddy Harris, ran the Bushito Game for our happy band of tabletop warriors.