The Japan Sports Association (JSA) is set to relocate to a building on the site of the Tokyo 2020 Olympic Stadium with construction due to start in the summer of 2017.
The JSA is currently based at the Kishi Memorial Hall in Shibuya, built when Tokyo hosted the 1964 Olympic Games.
Its new headquarters are scheduled to be complete by the spring of 2019 and will house an Olympic museum, according to plans.
The museum will be located on the first and second floors of the 14-story building, which will also have space for the Japanese Olympic Committee (JOC) and other sports associations.
Construction costs are estimated at ¥10 billion (£59 million/$85.6 million/€76.7 million) and will be shared between the JSA and the JOC, according to plans.
Last month, the Japan Sports Council (JSC) announced it has signed a ¥2.5 billion (£14.5 million/$21 million/€19.1 million) contract with the constructors of Japan's capital's new National Stadium, which is being built for the 2020 Olympic and Paralympic Games.
The agreement was reached between the joint venture building the stadium, which includes architect Kengo Kuma, construction giants Taisei Corporation and Azusa Corporation, and the JSC after they agreed to meet construction deadlines.
Japanese organisers recently claimed that it would be ready by November 2019 after they brought the deadline for completion of the project forward by two months.
The JSC hopes the construction of the stadium will begin by the end of this year, which will come after the construction contract is completed.
A basic plan is due to be unveiled in May following consultation with the Tokyo 2020 Organising Committee and various sports federations in the country.
The stadium has been a major embarrassment for Tokyo 2020 organisers, with the saga starting when the initial design by Iraqi-British architect Zaha Hadid was axed due to rising costs.
A cheaper design by Kuma has been selected as the replacement, but he has now been embroiled in a plagiarism row with Hadid claiming that his effort has "significant similarities" with hers, which the architect has denied.
JSC Board member Takakuni Ikeda moved to allay fears that the plagiarism claims would affect construction, declaring "no matter how the negotiations go with Zaha Hadid Architects, we’ll look to make sure it gets built properly".
It was originally hoped that the stadium would be ready for the 2019 Rugby World Cup in Japan, the first-ever edition of the tournament to be held in Asia, but delays caused by the scrapping of the initial design mean this is no longer possible.