The organisers confirmed that a visitor from abroad who is involved in organising the Games had tested positive during a routine test on Friday. The person's nationality was not revealed due to privacy concerns.
The 2020 Games, postponed for a year due to the global pandemic, is being held mostly without spectators and under tight quarantine rules.
Japan's public has been lukewarm about the Games amid a resurgence in new coronavirus infections and worries that an influx of visitors may create a super-spreader event, straining an already-stretched medical system. Only around 20% of the population is fully vaccinated.
Tokyo 2020 President Seiko Hashimoto acknowledged the public's concerns.
"I understand that there are still many worrying factors. Organisers must try to make sure that people will understand that these games are safe and secure," she told a news conference on Saturday.
So far, more than 40 people involved in the Games, including both domestic and foreign nationals, have tested positive. The latest case is the first at the 44-hectare athletes' village on Tokyo's waterfront, which is where a majority of the 11,000 competitors will be staying.
Athletes are just starting to arrive for the Games which run July 23 through Aug. 8.
A key part of the anti-contagion measures is daily saliva testing of the athletes who take part, as well as frequent testing of others involved in the event. Visitors' movements are also due to be monitored and restricted.
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