Three athletes, two of them staying at the Olympic Village, have tested positive for COVID-19, the Games Organising Committee announced on Sunday, the development adding to the scepticism around the troubled event which opens on July 23.
It is the first instance of athletes staying at the village catching the infection.
Their identities have not been revealed by the organisers.
The third infected athlete is staying at a designated Games hotel.
A total of 10 cases were detected on the day, including five "Games concerned personnel", one contractor, and a journalist, according to the COVID-19 Positive Case List uploaded by the OC here.
The total number of Games-related COVID cases have now risen to 55 as per the OC records.
"When there is a positive COVID 19 case - it means action.
There is a clear procedure to identify close contacts.
A case is not just data in a spread sheet but leads to action, including immediate follow-up testing," International Olympic Committee's (IOC) Games Executive Director Christophe Dubi stated.
"We can safely say that 40,000 COVID 19 tests have been carried out before coming to Japan for 18,000 Games participants.
Then there is the screening on the airport followed by regular screening, testing for athletes every day," he added.
The organisers did not specify whether the two infected athletes staying at the village will be quarantined elsewhere.
"Since 1 July more than 18,000 games participants arrived from overseas.
All of them had at least 2 negative tests before arrival.
When they arrived, they had another test.
When they are here, there is a strict testing regime in place," said Pierre Ducrey, IOC Games Operations Director.
"The participants of the Olympic Games are the most controlled population in the world," he added.
The development comes a day after a non-athlete at the Village tested positive for the dreaded virus and was shifted out of the premises.
".we believe we have the situation under control.
As such, properly if cases are found, the individuals are isolated and we trace all close contacts if there are any other cases, that's what is most important," Hide Nakamura, chief Games delivery officer for Tokyo 2020, said in a press conference.
"Even with all measures fully taken, there will be some positive (coronavirus) cases.
Under the coronavirus situation which encompasses the entire world, so it is inevitable that there will be cases.
"What is important is that when such cases arise, we properly systematically isolate them so that there will be no further transmissions.
The first batch of Indian athletes for the Games arrived here this morning.
The 88-strong Indian delegation comprised, archers, the two hockey teams, table tennis players and swimmers among others.
The shooters and the boxers also landed from their respective training bases in Croatia and Italy this morning.
The Games will be held behind closed doors as infections soar in the Japanese capital, which has been recording more than 1,000 cases per day for the past few days.
Despite the scepticism, IOC President Thomas Bach has insisted that the Games pose "zero risk" for the residents of Olympic village and the Japanese people in general.
The Olympic Village on Tokyo Bay will house 11,000 Olympic athletes and thousands of other support staff.