The race was due to take place on 10 October, as the third leg of a tripleheader after Russia and Turkey.
A decision on whether or not the race would go ahead was expected in August after all parties were able to review how the Olympic Games unfolded in Tokyo.
No further updates have been given on possible changes to the 2021 F1 calendar, which is understood to be very flexible at this stage, with various permutations under consideration.
However, F1 has options to keep up the numbers and will provide further news in the coming weeks.
An F1 statement said: “Following ongoing discussions with the promoter and authorities in Japan the decision has been taken by the Japanese government to cancel the race this season due to ongoing complexities of the pandemic in the country.
