Asian history buffs: ninja villages?

My global studies teacher (a well known head case) mentioned the other day that there were, in feudal Japan, hidden "ninja villages" of men and women who had ran away to escape the government.  Can anyone give me some sort of verification on this?

Ninja is basically based on myth and propaganda to expand the ninja mystery and renownedness across Japan. There were no real magic or secret villages, merely schools and organizations that taught Ninjitsu. People follow the idea that ninjas were these magical incredible superhumans. This is basically due to Anime and Japan indulging in their history making it seem greater than it really was. In Europe there wer Thieves and Rogues who were sometinmes exxagerrated as the same thing, but they all deviated from reality. Ninjas were merely Paid assassins and Sabotuers who used methods and unorthadox attack such as powder and camoflauge. They also had alot of knowledge of the body an knew where to place attacks and how to avoid detection. These strange fighting styles led to the ideal that they were mystical and had special villages when all one really had to do was enroll with a secret cabal or school trained for espionage and other tactics. But they were nothing more than crafty ordinary farmers and bandits.