The cases will heighten concerns over the Olympics, which are facing opposition in Japan over fears that they will bring new cases to a country that is already battling a wave of infections.
A daily new case count revealed that two athletes tested positive in the Village and one elsewhere. They arrive the day after an unidentified person, who was not a competitor, became the first case in the Village.
The Olympic Village, a complex of apartments and dining rooms, will host 6,700 athletes and officials at its peak when the 2020 Games, delayed last year by the pandemic, finally begin.
The Tokyo Olympics, which will be held largely behind closed doors to prevent infections, are unpopular in Japan, where opinion polls have consistently shown a lack of support.
On Saturday, International Olympic Committee chairman Thomas Bach called on Japanese fans to support the Games, saying he was “very well aware of the skepticism” surrounding the event.