It is the first coronavirus infection detected among athletes arriving for the Olympic games, which open on July 23.
The athletes arrived late on Saturday at Tokyo’s Narita airport and were all fully vaccinated with the AstraZeneca jabs and had negative PCR tests before boarding, the Asahi newspaper reported, quoting an anonymous Cabinet Secretariat official.
Yasutoshi Nishimura, a minister in charge of economic policy, told NHK TV Sunday that the government was looking into what had happened with border controls.
The team member who tested positive was not identified.
The eight other members of the team left early on Sunday by bus for host town Osaka.
The Ugandan team are the second team to arrive for the Olympics after the Australian women’s softball team, to arrive for the Olympics.
Uganda is seeing a rise in Covid-19 variants and has tightened lockdown measures. About 590 deaths have been reported, although this is likely an undercount due to the lack of testing.
Despite concerns about holding the Olympics during a pandemic, the International Olympic Committee, Tokyo organisers and Japanese government have insisted the games can be held safely.
“Let’s all wait a minute,” opposition lawmaker Renho tweeted. “This time, nine people arrived. For the Olympics, 100,000 people will be arriving. This is no time to be talking about how this will be a moving experience for our children.”
People flying into Japan are required to quarantine for two weeks upon arrival. But Olympic teams are not subject to the same border controls.
Fans from abroad were banned several months ago.
Organisers of the games are expected to decide on Monday whether local fans will be allowed in the stands. Plans for mass public viewing sites in Tokyo were abandoned on Saturday.
In Japan, daily cases are growing by several hundred. The country's state of emergency to control the spread of the virus ends on Sunday.
There has been no lockdown but restrictions, which have lasted for most of this year, focused on having restaurants and stores close early, limiting crowd sizes, and asking people to social distance, work from home and wear masks.
The vaccination rate in Japan is the slowest among developed nations, with about 6% of the population fully vaccinated.