The finger has been pointed at the Games that have brought competitors, press and officials from all over the world to a country where only 26% of the population are fully vaccinated.
But officials have denied a link between the Games and the surge in Covid cases while the International Olympic Committee (IOC) said the public should be reassured by the strict measures being taken to contain any cases connected with the Games.
Japan has kept its cases and deaths lower than many other countries since the outbreak of the pandemic, but its seven-day rolling average is growing and now stands at 28 per 100,000 people nationwide and 88 in Tokyo. This compares to 18.5 in the United States, 48 in Britain and 2.8 in India, according to data from Johns Hopkins University.
On Thursday, Tokyo, which has been under its fourth state of emergency since July 12, reported 3,865 new cases, up from 3,177 on Wednesday and double the numbers a week ago, setting an all-time high since the pandemic began early last year.
The Olympics faced widespread public opposition and concern the Games could worsen the outbreak. But Japan’s vaccine minister Taro Kono insists there is no evidence of the coronavirus spreading from Olympic participants to the general public.
"As far as I'm aware there's not a single case of an infection spreading to the Tokyo population from the athletes or Olympic movement," he told reporters.
"We have the most tested community probably anywhere... in the world, on top of that you have some of the toughest lockdown restrictions in the athlete's village," he added.
Meanwhile, top government medical adviser Dr Shigeru Omi cited the Olympics and summer holidays as reasons behind the acceleration in cases.
“The biggest risk is the lack of a sense of crisis and without it, the infections will further expand and put medical systems under severe strain," he said.
Tokyo officials said on Thursday that two foreign Olympic athletes are currently in hospital with Covid-related conditions while 38 others are self-isolating at designated hotels in the city.
Nationwide, Japan reported more than 9,500 confirmed cases, also a record, on Wednesday. The total number of infections now stands at about 892,000. Some 15,000 people have died with Covid in Japan.
Dr Norio Ohmagari, director of the Disease Control and Prevention Center, said Tokyo’s surge is “heading toward an explosive expansion we have never experienced before.”
The rising cases is an alarming backdrop to a Games being played out in a pandemic that stands precariously on a knife edge.
Just how much the domino effect of positive test could have on this delayed Olympics could have was exposed when the entire Australian track team were briefly quarantined after American pole vaulter Sam Kendricks tested positive for coronavirus.
Two-time world champion and the American record holder was one of dozens of athletes on the training track this week. After three Australian athletes reported having casual contact with Kendricks, Australia announced it had put its entire 54-person team (41 athletes and 13 officials) in isolation as they awaited testing.
A few hours later, the Australian Olympic Committee announced the trio had tested negative and all but those three were let out of quarantine.
Kendricks is not the first athlete to have tested positive for Covid. A recent wave of positive tests has brought the current total number of positive Olympic Covid-19 tests to 148 including 12 security guards.
Six athletes from the Team GB squad were forced to self-isolate after sharing a flight with someone who has since tested positive for Covid.
The estimated 70,000 athletes, coaches, staff, officials and media descending on Tokyo between July to August for the Olympic and Paralympic Games are subjected to strict rules including a rigorous testing programme.
As well as daily testing, there are mask mandates, social-distancing procedures and isolation bubbles in place to contain any outbreaks of the virus.
It is also estimated around 80% of Olympic participants are also fully vaccinated.
British long jumper Jazmin Sawyers posted a video on Twitter which showed the stark reality of life for athletes competing in a pandemic Games.
In the minute long clip, she is shown taking her daily PCR test which must be done before 10am.
Then, athletes take their temperature and log it on the app.
They must wear masks at all time except when training or eating - and eating is done behind screens.
Competitors, coaches and officials are allowed out of their team hotel just once a day on a supervised walk that covers no more than 100 metres. They are restricted to a few floors of the hotel - and if they want to pop out for a bit of fresh air they allowed onto the balcony but must wear a mask.