There are several types of traditional, Japanese music (hogaku).
Some of them are listed below:
Ancient court music from China and Korea. It is the oldest type of Japanese, traditional music.
Music played with the Biwa, a kind of guitar with four strings.
Music played during Noh performances. It basically consists of a chorus, the Hayashi flute, the Tsuzumi drum, and other instruments.
Music played with the Koto, a type of zither with 13 strings. Later also accompanied by Shamisen and Shakuhachi.
Music played with the Shakuhachi, a bamboo flute that is about 55 cm long. The name of the flute is its length expressed in shaku an old Japanese unit of length.
Music played with the Shamisen, a kind of guitar with only three strings. Kabuki and Bunraku performances are accompanied by the shamisen.
Japanese folk songs.
(extracted from http://www.japan-guide.com/e/e2113.html)