Just over a week before the opening ceremony, new cases linked to the Games and spiking infections in the host city highlight the risks of staging the world's biggest sports event during a pandemic even without spectators in sports venues.
Seven staff at the hotel in Hamamatsu city, southwest of Tokyo, had tested positive for the coronavirus, a city official said.
But a 31-strong Brazilian Olympic delegation, which includes judo athletes, are in a "bubble" in the hotel and separated from other guests and have not been infected.
The host city Tokyo, where a state of emergency has been imposed until after the Games end on Aug. 8, also recorded 1,149 new COVID-19 cases on Wednesday, the most in nearly six months.
Highly contagious virus variants have fuelled the latest wave of infections, and failure to vaccinate people faster has left the population vulnerable.
Medical experts are worried that Olympic "bubbles", imposed by Tokyo 2020 Olympic officials in an effort to keep out COVID-19, might not be completely tight as movement of staff servicing the Games can create opportunities for infection.
The Olympics, postponed last year as the virus was spreading around the world, have lost much public support in Japan because of fears they will trigger a surge of infections.
International Olympic Committee (IOC) President Thomas Bach praised the organisers and the Japanese people for staging the Games in the midst of the pandemic.
"These will be historic Olympic Games ... for the way how the Japanese people overcame so many challenges in the last couple of years, the great east Japan earthquake and now the coronavirus pandemic," Bach told reporters after meeting Prime Minister Yoshihide Suga.
When Japan was awarded the Games in 2013, they were expected to be a celebration of recovery from a deadly earthquake, tsunami and nuclear accident in 2011.
Japanese leaders had hoped the re-scheduled Games this year would be a celebration of the world's victory over the coronavirus but those celebrations are on hold as many countries struggle with new surges of infections.
The coronavirus cluster at the Brazilians' hotel was found during routine screening required before staff started work, said city official Yoshinobu Sawada.
Many Olympic delegations are already in Japan and several athletes have tested positive upon arrival.
The refugee Olympic team has delayed its travel to Japan after a team official tested positive in Qatar, the International Olympic Committee said.
Members of the South African rugby team are in isolation after arriving, as they are believed to be close contacts with a case on their flight, said Kagoshima city, which is hosting the team.
The 21 members of the South African squad were due to stay in the city from Wednesday, but that plan has been halted until further advice from health authorities, said city official Tsuyoshi Kajihara.
Global interest in the Tokyo Olympics is muted, an Ipsos poll of 28 countries showed, amid concerns over COVID-19 in Japan and withdrawals of high-profile athletes, with the host country among the most disinterested.
The poll released on Tuesday found a global average of 46% interest in the Games, and in Japan 78% of people were against the Games going ahead.
With spectators barred from all Olympic events in Tokyo and surrounding regions officials are asking people to watch the Games on television and keep their movements to a minimum.
"Billions of people around the globe will be glued to their screens and they will admire the Japanese people for what they have achieved under these very difficult circumstances," Bach said.
Among those will not be competing in Japan is former world number one golfer Adam Scott. He questioned whether holding the Tokyo Olympics was a responsible decision, pointing to fear among people in Japan as it battles its resurgence of infections.
Switzerland's Roger Federer became the latest big name in tennis to withdraw from the Tokyo Olympics after the 20-times Grand Slam champion said on Tuesday that he had picked up a knee injury during the grasscourt season.