The Olympic Village situated at the Tokyo Bay house about 11,000 athletes during the Olympics and thousands of other staff.
The 26-year-old becomes the third Tokyo 2020 athlete to test positive for the virus following South African footballers Thabiso Monyane and Kamohelo Mahlatsi.
Czech Republic Olympic team confirmed the development on Monday saying that the players have no symptoms.
“He has absolutely no symptoms. We are dealing with all the details and naturally the anti-epidemic measures within the team,” said Martik Doktor, Czech Olympic team head in a statement.
Earlier on Saturday, the Czech Olympic Committee reported a staff member had tested positive for the virus after arriving in Tokyo on a charter flight from Prague.
“Unfortunately, beach volleyball player Ondrej Perusic has a positive finding from a sample taken during daily testing in the Olympic village on Sunday,” Martin Doktor, sports director of the Czech Olympic Committee, said in a statement.
“It is still fresh information and everything is evolving quickly. We are solving details, including the sport impact.”
The total number of Games-related cases now stands at 58.
Postponed for a year due to the global pandemic, the Tokyo Olympics will run from July 23 through Aug. 8.