Japan has attributed about 3,800 deaths to COVID-19 in a country of 126 million.
Asked how clean he thinks the Games will be the 23-time Olympic gold medalist bluntly told CNN Sport's Don Riddell: "Four or five" out of 10.
Although the length of the 121-day torch relay will not be shortened, the number of staff present and use of official vehicles will be reviewed.
The IOC and organizers have also said the Olympics will not be postponed again and would be canceled.
The Olympics could be canceled if the Covid-19 pandemic continues into next year, according to the Tokyo 2020 president.
Local estimates say the postponement will cost between $2 billion and $6 billion with Japanese governments picking up almost all the bills.
The Olympics draw 11,000 athletes and 4,400 Paralympic athletes and large support staffs from 206 national Olympic committees.
Through Thursday, Japan had reported about 3,300 cases of coronavirus with 74 deaths, according to the health ministry.
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The Olympics are set to begin July 24 in Toyko.