The nine-member delegation including boxers, coaches and officials, arrived on Saturday just over a month before the pandemic-postponed Games.
But despite being vaccinated and testing negative before travel, a coach tested positive during screening at Tokyo’s Narita airport.
The coach was isolated, and the rest of the squad was allowed to leave for their training base in Izumisano, southern Osaka.
“But our local healthcare centre questioned the eight members and designated them as close contacts with the person who tested positive,” a city official told AFP.
“Now we are requiring them to stay inside the hotel until July 3,” the official said, adding that the city was still looking into the possibility of allowing training outside the hotel.
The eight members have so far tested negative and are in good condition, the official said.
They have not left the hotel since arriving or had contact with others, he added.
The team, which is the second to arrive in Japan for the Games after Australia’s softball players, was originally due to arrive in Japan on June 16.
But their flight was cancelled following a surge in Covid-19 cases in Uganda, local media said.
The coach was the first positive virus case among officials and other Olympic participants arriving in recent days, local media said.
Last week organisers released virus guidelines for athletes as part of their effort to hold the Games safely.
Athletes have to test negative before travel to Japan, as well as on arrival, and will be tested daily while in the country.
They face being kicked out of the Games if they break rules including mask-wearing and avoiding travel except between their venues and the Olympic Village.