Occasionally the Komusō-Shakuhachi is also known as "Zen Shakuhachi", especially outside of Japan. It seems that a special relationship with Zen Buddhism, which has become so popular in the West, is to be emphasised. Unfortunately, in the choice of this term, not only ignorance of the facts, but often also commercial interests play a role ("Zen sells"). For the historical Komusō, a substantive relationship with the Zen school is scarcely verifiable, and for the modern Komusō, the term "Zen-Buddhist" is simply inaccurate.

Historically, the only loosely organised group of Shakuhachi-playing begging monks was formally attributed to the Rinzai school of Zen in 1677. The "Legend of the Kyotaku" played an important role in this formal "conversion" of the Komusō movement into Zen. The religious theory and practice of the Komusō was, however, by no means purely Zen Buddhist in the narrower sense, but is influenced by many other aspects of Japanese religiosity.

For the modern Komusō-Shakuhachi players it is true that they were in many cases not formally Zen-Buddhists at the time of their foundation or even today. Many of their most prominent representatives belonged to other Buddhist denominations. Higuchi Taizan 樋口対山 (1856-1914) and Uramoto Setchō 浦本浙潮 (1891-1965) were two significant Shakuhachi players and had a great influence on the reestablishment of the Komusō movement. But Taizan had originally been a follower of the Jōdo Shin School of Pure Land Buddhism, and converted later to the Lotus Buddhism of the Nichiren School, and Setchō was an enthusiastic follower of the Jōdo-shin school, that is an Amida-Buddhist.