TOKYO—Like Olympic villages of past years, Tokyo’s version in 2020 will feature new buildings to house athletes and buses to ferry people to competition venues. But if Tokyo’s governor has his way, it will all be powered by a new energy source: hydrogen.

“The first Tokyo Olympics, 50 years ago, left a bullet-train system as a legacy. I want to leave a hydrogen society as a legacy for the next Tokyo Olympics,” Gov. Yoichi Masuzoe said in an interview.

Tokyo...