The Master's program offers five majors: Instrumental Music, Vocal Music, Composition, Musicology, and Music Education. Together with the Virtuoso course in the Instrumental Major and Vocal Major, a Piano Collaborative Arts Course has been established to train artists who create music in cooperation with ensembles. Applicants must have graduated from a four-year course or have equivalent or higher academic qualification.

Although this is a two-year program, it is possible to study for four years. Students are permitted to take a leave of absence (to study abroad etc.) for a total of three years. With an emphasis on the lessons and research of each major, the techniques of ensemble and musical accompaniment will also be enhanced. Students also engage in an investigation into specializations through unique lectures on musical history and their chosen field as well as theoretical study and analysis.

Those who complete at least 30 credits of a given course and have passed the major practical examination, successfully completing their master's thesis, will receive a master’s degree in Music or Musicology. In the Virtuoso course, students can attain a master's degree by passing a performance examination without needing to produce a master's thesis. Graduates go on to become professional performers, researchers and educators.

In addition, a student taking the Instrumental Music course (piano), including the Virtuoso course, and who achieves the best grades at the time of graduation will receive the Kreutzer Prize. This was established to commemorate the achievements of the late Professor Leonid Kreutzer, who made a significant contribution to the Japanese music world.