"We reached the conclusion that unfortunately, it is difficult to organise the event... after several cases (of the virus) were confirmed in Tokyo," the Tokyo Marathon Foundation said in a statement.
The decision will not affect elite runners, including elite wheelchair participants, the organisers said.
But they only account for around 200 of the tens of thousands of people who had registered for the 1 March race.
The cancellation comes after Japanese government officials warned the spread of the virus in the country entering "a new phase".
At least 65 cases have been diagnosed in Japan, excluding hundreds of infections aboard a cruise ship quarantined off the coast.
On Sunday, the health minister warned citizens to avoid large crowds and non-essential gatherings, sparking speculation that the marathon would be cancelled.
A public gathering for the birthday of Emperor Naruhito that was scheduled for 23 February has also been cancelled on virus fears.
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