Setting aside the fact for a second that the question doesn't really make sense, "Ninjas" weren't "against" the Samurai. There were no secretive black clad clans of supernatural martial artists in Japan. There were spies who were sometimes Samurai, who were called Shinobi, who essentially inspired the concept of ninja. And "Imperial Japan" is the country of Japan as it was referred to during and up to WWII. So that part of your question makes no sense.