The infected person has now been isolated in a government-controlled facility while the other eight went on to their base in Osaka for further preparations.
Prior to departure, all members of the Ugandan squad had received two doses of vaccine from Astra Zeneca and tested negative 72 hours before departure, writes Reuters.
The organizer has previously banned foreign audiences from the championship.
Tomorrow, it will be decided whether the Japanese will be allowed to see the competitions on site.
Can be anything from zero to 10,000 in the stands
The organizer is looking at a solution with up to 10,000 spectators per arena, while health experts linked to the government have warned against admitting spectators at all.
Regardless of the decision on Monday, the organizer plans for 20,000 spectators at the inauguration on July 23.
The games kick off with football on July 21.
The Ugandan squad is the second to land in Tokyo.
As early as June 1, Australia's women's softball team came to Japan to prepare.