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The resident - who tested positive on Friday - is not an athlete and is described simply as a non-resident of Japan and a "games-concerned personnel" due to confidentiality purposes.
"In the current situation, that positive cases arise is something we must assume is possible," said Toshiro Muto, the CEO of the Tokyo organizing committee.
The person will now self-isolate for 14 days, with the Games started in six days' time.
The positive result is the 44th since July 1 among "contractors" and "games-concerned personnel" but Friday's was the first from the Olympic Village.
Around 11,000 athletes will be housed in the Tokyo Bay hub for the Games, along with thousands of staff.
IOC President Thomas Bach insisted this week there was "zero" risk to athletes in the village. Tokyo on Thursday recorded the highest daily rise in cases in six months.