Originally from Osaka, Japan, Nakatani moved to the United States in 1994. Based in the Boston area, he began performing and releasing self-issued cassettes during the late '90s. He was an early member of Bhob Rainey and Greg Kelley's improvisational group Nmperign, and additionally collaborated with musicians such as Michael Bullock and Curt Newton. He began collaborating with saxophonist Assif Tsahar during the early 2000s, performing as part of his New York Underground Orchestra, whose debut The Labyrinth appeared in 2002. Nakatani also participated in projects such as Blue Collar (with Nate Wooley), Masashi Harada Condanction Ensemble, and Cyclorama, additionally performing in the Billy Bang Quintet. 13 Definitions of Truth (with double bassist Peter Kowald) was issued by Quakebasket and Locust Music in 2003. Nakatani's solo album Green Report 12 was released through his own HH Production in 2004; the imprint also released Six Improvisations (For Guitar Bass and Drums), the debut by MAP, which featured Nakatani along with guitarist Mary Halvorson and bassist Clayton Thomas. Come Sunday, a collaboration with Tsahar, appeared on Hopscotch Records that year. Nakatani worked with Ricardo Arias and Vic Rawlings under the name N.R.A., releasing two CDs in 2004-2005, and additionally played in From Between Trio with Jack Wright and Michel Doneda.
In 2005, Nakatani collaborated with bassist Todd Nicholson and guitarist Eiji Obata, releasing the bossa nova-influenced Mott Haven under the name Yukijurushi. Solitude, with Tsahar and KJLA String 4tet, was released by Hopscotch in 2006. In 2007, Nakatani released solo disc Primal Communication as well as two collaborations with Gary Hassay and Dan DeChellis (the trio released a third effort, Ritual Joy, in 2010). Nakatani worked with Neil Davidson and Raymond MacDonald as Aporias Trio, releasing Entre Nous in 2009. MAP's Fever Dream, featuring bassist Reuben Radding instead of Clayton Thomas, was released by Taiga in 2010. Also during the year, Nakatani's collaboration with Forbes Graham, Essences, was issued by Blaq Lghtn, and solo album Abiogenesis appeared on HH. In 2011, Nakatani released collaborative albums with Doneda, Kaoru Watanabe, and Eugene Chadbourne, in addition to appearing on Rafael Toral's Space Elements Vol. III. Ritual Inscription, a live collaboration with Kris Tiner and Jeremy Drake, was issued by Epigraph Records in early 2012. That year, Taiga released Nakatani Gong Orchestra, the eponymous debut by Nakatani's performance ensemble. He also guested on Blues Control's Valley Tangents, issued by Drag City.
2013 releases included 3 on a Thin Line (with Harold Rubin and Barre Phillips), Anatomy of a Moment (with Shane Perlowin), and solo album Present Presence. Solo releases Confirmation and Gong appeared in 2015, as did Charades (with Doneda). The following year, Nakatani released Live in Oita 2016, a collaboration with Acid Mothers Temple leader Makoto Kawabata, and I Got It Bad, a duo with Tsahar. Nakatani Gong Orchestra's Live Concert at Silo City appeared in 2017. In 2018, RareNoise released The Unknowable, Nakatani's collaboration with David Liebman and Adam Rudolph. The year also brought recordings with Mark Weaver (Weaver Nakatani) and Jeff Coffin (Flight). ~ Paul Simpson, Rovi