Of course the actual Ninja came from and originated in Japan....But the Japanese refined other's culture. Something they are still masters at.
I would think that groups like the Thugees of India could be considered the predecessors(sp?) of Ninja...they were a sect of Kali worshiping people in the Calcutta area that were notorious for lurking in the shadows and stealing people from their homes to be sacrificed..... Certainly NOT Ninja.....but if you are looking for where the techniques and ideas started...India is the motherland of asia.

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Watashiwa Yagyu Jubei desu! Ganbate!