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?

>>10

If they're so normal, how do explain that one time when there was a ninja eating at a diner, and then someone dropped a spoon, so the ninja flipped out and killed the entire town?