The truth is that the origins of the shakuhachi is a mystery. We are not historians, nor claim to know the answer to this question, however, the following is a compilation of shakuhachi history sewn together by Meredith in her quest of understanding the origins of this beautiful instrument.
The Shakuhachi flute has been traced back as far as ancient Egypt and is thought to have migrated through India and China before being brought back to Japan by monks who were studying abroad in China during the 6th century.
The Shakuhachi that was brought back from China was a six holed flute that was traditionally used to play chamber music for those privileged with wealth and royalty. As the result of isolated evolution in Japan, the Shakuhachi developed into a five hole flute by the time it reached the hands of the Komoso monks in the 1600s. Wearing woven baskets on their heads as a symbol of their detachment from the material world, the Komoso, also known as straw-mat monks, lived a life of poverty and used the Shakuhachi in their practice of zazen. Zazen later became known as suizen, or blowing zen. These monks would work on mastering their meditative breath, also called Kisoku, through the playing of the shakuhachi. The Shakuhachi was considered a religious tool among the Zen monks rather than a musical instrument. They believed that by mastering their breathing with shakuhachi, it would lead them to the path of enlightenment, becoming a Buddha of one sound, connecting them to all planes of existence. The monks felt it was not only the flute player that could obtain enlightenment, but also those who listened to the sound of the Shakuhachi. The Komuso monks lived a migrating life, playing their flutes wherever they went. They grew in numbers over the centuries and were joined by many sword-less samurai during the civil wars of the 15th and 16th centuries.
During the rule of Tokugawa, also known as the Edo Period or rule of the Shoguns the Komoso monks formed a religious sect claiming ties to Fuke, a famous Chinese Zen monk who lived during the 9th century. The government accepted the tie to Fuke in 1614 enabling the establishment of the Fuke Sect, which was accepted as a branch of Rinzai Zen. At this time the Komoso changed their names to the Komuso, the monks of emptiness. The Komuso made an agreement with the government that they would have the sole right to solicit alms by playing the Shakuhachi and in exchange of the agreement the government sent spies for the Shogun in the disguise of monks, which seemed a rather easy disguise due to the woven baskets worn on the monks heads which hid their identity. Legend says that in response to the government sending spies dressed as monks, difficult Honkyoku pieces became tests or trials for the monks. If they were played well you were considered a real monk, but if they were played poorly, you were likely to be beaten or killed in unfriendly territory as being a suspected spy. During this time the shakuhachi began to be made with four rows of the bamboo roots still attached, so that it could be used as a club in self defense if necessary. Having these four rows of roots attached to the end of the flute narrowed the opening of the flute and enabled the second octave to be played in pitch. The shakuhachi's sound changed drastically due to the new tapered bore configuration.
The Fuke Sect of monks was dissolved around 1871 when the Tokugawa government fell and the Meiji Restoration began. Because of the special arrangement the Fuke Sect had with the Shoguns the Meiji would not honor the Fuke sect in order to weed out and eliminate spies and the Shoguns holdouts. The playing of the shakuhachi became forbidden and its use went underground. When the Meiji government did permit the use of the shakuhachi again it was played as an accompanying instrument to the shamisen and koto. Many of the honkyoku and important documents were lost during the hiding. It wasn't until 1883 in Kyoto, Japan that the shakuhachi was revived by the Myoan Society at the old Fuke Temple, Myoan-ji. This society is responsible for much of the traditional shakuhachi music we have today.
The Shakuhachi has gone through many changes over the last few centuries. In the 20th century it was very much influenced by western music and a new type of shakuhachi music was born called Tozan. Shakuhachi is now heard in modern day jazz, it has been featured in Hollywood's soundtracks, as well as once again being enjoyed as classical orchestra chamber music.