Elected members are confirmed by the Government of Japan, a method similar to that of the National Academy of Sciences in the United States, upon which the structure of the SCJ was based.

It was officially founded in January 1949 to function as an independent scientific statutory body under the jurisdiction of the Prime Minister of Japan.

[6] In 2020, Prime Minister Yoshihide Suga rejected six candidates nominated for the council, drawing criticism from opposition lawmakers and academics.

Representing the resolution of the council's executive board, President Onishi held a press conference on 23 July condemning the official decision.

He expressed the council's belief that the dissolution of these disciplines "may result in higher education in Japan losing its breadth and depth.