Japan as a whole also beats France, with 32 establishments granted the maximum grade, against 25 in the guide's home country.
Of Tokyo's 160,000 restaurants, 16 were awarded top marks, 52 got two stars and 179 were deemed worthy of one star by the authors of the Red Guide.
Paris has just 10 three star eateries.
While most of those included in the book serve Japanese food, a Korean restaurant was awarded two stars, while two French restaurants got top honours.
A guide to western Japan released last month propelled the country into the world top spot for haute cuisine, with 15 top rated restaurants in cities including Kyoto, Osaka, Kobe and the former capital Nara.
"Japan is a unique country with many cities full of high level cuisine," said Bernard Delmas, president of Michelin in Tokyo, last month.
"This is why, though we reach the fifth anniversary of the arrival of the Michelin guide in Japan, we continue to discover new stars to introduce to our readers."