The scrapping of the tournament, scheduled to take place between October 5 and 11 in Tokyo, raises some doubts over the traditional "Asian swing", when the ATP tour takes in several tournaments in Asia.
According to a revised schedule published by the ATP to take account of coronavirus, tournaments were also due to take place in the Chinese cities of Chengdu, Zhuhai, Beijing and Shanghai.
Japan Open organisers said on their website it would be the first time the tournament had been cancelled since 1972.
They said they considered various options, including restricting entry and holding the competition in empty stadiums, but eventually decided safety could not be guaranteed.
"Given concerns about a second wave of the infection both in Japan and overseas, we came to the anguished conclusion that we had to cancel," they said.
Japan has been relatively lightly affected by the coronavirus compared to many western countries, with just over 900 deaths from 17,000 cases.
But a recent spate of cases in Tokyo has raised fears of a possible second wave.
There was no indication that a WTA event scheduled for November had yet been cancelled.
Like all sports, tennis has been devastated by the coronavirus and is only gradually getting back on court.
The delayed French Open is due to start on September 27 — with fans in attendance — after being switched from its traditional May-June slot due to the pandemic.
With the US Open already confirmed to start on August 31, the ATP announced its tour would resume in Washington from August 14.
The women's tour will restart in Palermo, Italy, on August 3.