Media reports said Ssekitoleko, who did not meet Olympic standards in the latest international rankings, was to return home next week. Kyodo News agency said he left a note saying he wanted to stay in Japan and work.
The mayor of Izumisano, Hiroyasu Chiyomatsu, said officials had received reports of possible sightings of Ssekitoleko at a nearby train station.
The pandemic-delayed Olympics begin on July 23 despite mounting concern about Tokyo's upsurge of infections. The host city on Friday reported 1,271 cases, after hitting a six-month high at 1,308 the day before.
The Ugandan team has featured before in Japan's health and surveillance system.
On their arrival on June 19 at Narita International Airport, a member of the team tested positive and was quarantined there, while the remaining eight members were allowed to travel more than 500 kilometres (300 miles) on a chartered bus to Izumisano, their pre-Olympics camp in the western prefecture of Osaka.
Days later, a second member of the team from East Africa tested positive for the virus, forcing seven town officials and drivers who had close contact with the team to self-isolate. Health officials said both infected Ugandans had the delta variant.
Both team members have since ended their quarantine requirement and the team has been training since July 7.
The case prompted the Japanese authorities to step up border controls and change isolation policy to require entire groups to quarantine in airport areas when any member tests positive.
While Japanese officials have required the use of health and location apps, and restricted activity in a "bubble" to fully isolate athletes from the Japanese public, violations have been reported.
Monitors pledged earlier by Olympic Minister Tamayo Marukawa have not been seen operating at a number of hotels. Marukawa told reporters Friday that she is asking organizers to strengthen measures and increase surveillance staff at hotels to make sure rules are followed.
