The Masters Degree currently takes many forms internationally and its content is equally diverse. The policy of IGSES requires the candidate student to hold a Bachelors degree in an appropriate subject area before being allowed to undertake Masters level study. Typically, the Grade Point Average (GPA) of the Bachelors Degree is utilized to screen candidate students especially for demanding special programs that are funded by MEXT.

The Global Course Masters Degree closely mirrors the Normal Course Masters Degree with the primary difference being that all teaching and assessment is carried out in English instead of Japanese. All five departments ASEM, MMS, AEES, EEE and ESST, require the student to accumulate 30 credits from the available lecture courses, professional activities, research work and thesis evaluation. However, in the case of the Green Asia Program (GA) at least 40 credits are required.

After the accumulation of all necessary credits, the student must deliver an oral presentation detailing the content and achievements of their research work and submit a Masters Thesis to the thesis review committee. Generally, the duration of the Masters Programs offered by IGSES are approximately 2 years, although a student may be allowed to pursue early graduation if their achievement was deemed to be particularly outstanding by the thesis review committee. There are no strict publication requirements for successful graduation, however it is typical within IGSES for Masters students to achieve 1 or 2 peer reviewed publications before or shortly after graduation.

As is the case with the Doctoral Degree, the four departments ASEM, MMS, AEES and ESST are able to award 3 types of Masters Degree, Master of Engineering (MEng), Master of Philosophy (MPhil) and Master of Science (MSc). EEE is currently only able to award MEng and MPhil degrees. The student can select the type of degree to be awarded prior to their graduation, however the MPhil is rarely awarded by IGSES due to its obscurity in Japan. In practice there is absolutely no variation in the research content, coursework requirements, requisite credits or academic reputation between the three degree types.