- Orchestral Works
- Requiem for String Orchestra (1957)
- Music of Tree (1961)
- The Dorian Horizon (1966)
- Green (1967)
- Winter (1971)
- A Flock Descends into the Pentagonal Garden (1977)
- A Way A Lone II for string orchestra (version of A Way a Lone for string quartet)
- Rain Coming for chamber orchestra (1982)
- Dream/Window (1985)
- Twill by Twilight—In Memory of Morton Feldman (1988)
- Tree Line for chamber orchestra (1988)
- Visions (1990)
- I Mystère
- II Les yeux clos
- How slow the Wind (1991)
- Archipelago S. for 21 players (1993)
- Works for soloists and orchestra
- Arc Part I for piano and orchestra (1963–1966/1976)
- I Pile (1963)
- II Solitude (1966)
- III Your love and the crossing (1963)
- Arc Part II for piano and orchestra (1964–1966/1976)
- I Textures (1964)
- II Reflection (1966)
- III Coda ... Shall begin from the end (1966)
- November Steps for biwa, shakuhachi and orchestra (1967)
- Asterism for piano and orchestra (1967)
- Eucalyptus I for flute, oboe, harp and string orchestra (1970)
- Autumn for biwa, shakuhachi and orchestra (1973)
- Quatrain for clarinet, violin, cello, piano and orchestra (1975)
- Far calls. Coming, far! for violin and orchestra (1980)
- Toward the Sea II for alto flute, harp and string orchestra (version of Toward the Sea for alto flute and guitar (1981))
- To the Edge of Dream for guitar and orchestra (1983)
- Orion and Pleiades for cello and orchestra (1984)
- riverrun for piano and orchestra (1984)
- I Hear the Water Dreaming for flute and orchestra (1987)
- Nostalghia—In Memory of Andrei Tarkovsky for violin and string orchestra (1987)
- A String Around Autumn for viola and orchestra (1989)
- From Me Flows What You Call Time for five percussionists and orchestra (1990)
- Fantasma/Cantos for clarinet and orchestra (1991), winner of the Grawemeyer Award for Music Composition.
- Quotation of Dream for two pianos and orchestra (1991)
- Fantasma/Cantos II for trombone and orchestra (1994)
- Electronic and Tape Music
- Static Relief, magnetic tape (1955)
- Vocalism A・I, magnetic tape (1956)
- Water Music (1960)
- Kaidan (1964)
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- Chamber works
- Le Son Calligraphé I–III for four violins, two violas and two cellos (1958–1960)
- Ring for flute, terz guitar and lute (1961)
- Corona II for string(s) graphic work in collaboration with Kōhei Sugiura (1962)
- Arc for Strings graphic work (1963)
- Valeria for violin, cello, guitar, electric organ and two piccolos (1965)
- Eucalyptus II for flute, oboe and harp (1971)
- In an Autumn Garden for gagaku orchestra (1973/1979)
- Garden Rain for brass ensemble (1974)
- Waves for clarinet, horn, two trombones and bass drum (1976)
- Quatrain II for clarinet, violin, cello and piano (1977)
- A Way a Lone for string quartet (1981)
- Rocking Mirror Daybreak for Violin Duo (1983)
- Signals from Heaven—two antiphonal fanfares for two brass groups (1987)
- I Day Signal
- II Night Signal
- And then I knew 'twas Wind for flute, viola and harp (1992)
- Piano works
- Romance (1949)
- Lento in Due Movimenti (1950, unpublished/original lost—rewritten as Litany, 1989)
- Piano Distance (1961)
- Corona for pianist(s) graphic score (in collaboration with Kōhei Sugiura, 1962)
- Crossing graphic score (in collaboration with Kōhei Sugiura, 1962)
- For Away (1973)
- Les yeux clos (1979)
- Rain Tree Sketch (1982)
- Litany—In Memory of Michael Vyner recomposition of Lento in Due Movimenti (1950/1989)
- Rain Tree Sketch II—In Memoriam Olivier Messiaen (1992)
- Guitar
- Folios (1974)
- 12 Songs for Guitar (1974, 1977)
- The Last Waltz (1983)
- A Boy Named HIROSHIMA (1987)
- All in Twilight - Four pieces for guitar - written for Julian Bream (1987)
- Bad Boy (1961, 1992)
- A Pieces for guitar - For the 60th birthday of Sylvano Bussotti - (1991)
- Equinox (1993)
- In the Woods - Three pieces for guitar - (1995)
- Film scores
- Pitfall (Otoshiana), dir. Hiroshi Teshigahara (1962)
- Harakiri, dir. Masaki Kobayashi (1962)
- Woman in the Dunes, dir. Hiroshi Teshigahara (1964)
- Kaidan, dir. Masaki Kobayashi (1964)
- Assassination, dir. Masahiro Shinoda (1964)
- The Face of Another, dir. Hiroshi Teshigahara (1966)
- Samurai Rebellion, dir. Masaki Kobayashi (1967)
- Double Suicide, dir. Masahiro Shinoda (1969)
- Dodesukaden, dir. Akira Kurosawa (1970)
- Empire of Passion, dir. Nagisa Oshima (1978)
- Ran, dir. Akira Kurosawa (1985)
- Black Rain, dir. Shohei Imamura (1989)
- Rising Sun, dir. Philip Kaufman (1993)
- Other instrumental
- Masque, for two flutes (1959, 1960)
- Eclipse, for biwa and shakuhachi (1966)
- Voice, (1971)
- Itinerant—In Memory of Isamu Noguchi, (1989)
- Paths, for solo trumpet (1994)
- Air (1995, last published work)
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