The 1728 composition, called "Wedding Cantata BWV 216," was found among the papers of Japanese pianist Chieko Hara, who died in Japan in 2001 aged 86.
The work, written for the wedding of a daughter of a German customs official, was missing for 80 years.
Professors at the Kunitachi College of Music in Tokyo say they may release copies for future performances.
The eight-page handwritten composition contains soprano and alto parts with notes and lyrics written in German, Professor Tadashi Isoyama said.
It is not clear how Hara obtained the manuscript - its last known owner was a descendant of German composer Felix Mendelssohn.
However, researchers believe Hara may have obtained it from her husband - Spanish cellist Gaspar Cassado, who knew Mendelssohn's descendant.
Born in Eisenach, Germany in 1685, Bach is acknowledged as one of the world's most prolific composers and as a master of the baroque music style, report BBC.
The work was created for the wedding of a daughter of a customs official, Isoyama said. It was passed over from his family to collectors and musicians before reaching the family of German composer Felix Mendelssohn who had it until around 1926.
Experts, including Isoyama, believe Hara's Spanish husband received it from Mendelssohn's family, inform reuters.com
It was not clear how Hara came to acquire the score, the last known owner of which was a descendant of German composer Felix Mendelssohn, Isoyama said.
Researchers believe Hara, who spent much of her career in Europe, might have received it from her Spanish husband and cellist Gaspar Cassado, who knew Mendelssohn's descendant.
Isoyama's college purchased the work and is considering releasing copies of the score for further research and performance, according to news.com.au