Makoto Tamada was Japan's last rider to start on pole in 2004.
Nakagami took pole just two days after signing a new multi-year deal with Honda, and he becomes the season's sixth different pole-position rider.
Petronas Yamaha's Franco Morbidelli will start in second, while Suzuki's Alex Rins joins them on the front row. Rins' team mate and championship leader Joan Mir starts well back in 12th position. (Reporting by Rohith Nair in Bengaluru; Editing by Hugh Lawson)