The museum's collection includes ancient ninjutsu writings analyzed scientifically along with ancient ninjutsu weapons. The museum has audiovisuals, models and extensive static displays of the weaponry and techniques employed by ninja. There are over 400 ninja tools on display, including shuriken actually used in the time of the ninja. The museum also features a model village with tours and demonstrations of its features.
There is also a virtual version of the museum in Second Life.