Torrential rain failed to dampen Japanese enthusiasm as the flame touched down in the city which hosted the 1964 Games.
Amid heavy security, former baseball player Kazushige Nagashima was the first torch bearer on the 53-kilometre run which began near Tokyo Bay.
Olympic speed-skating champion Hiroyasu Shimizu and Kyoko Iwasaki, who won swimming gold at the 1992 Barcelona Games, were among 136 participants. Fifteen-year-old table tennis player Ai Fukuhara ran the final leg in drizzly conditions.
"I didn't tell my dad I was running today because he would have been really jealous," said Nagashima, whose father Shigeo will coach Japan's baseball team in Athens despite suffering a stroke in April.
The flame arrived in Tokyo from Melbourne after returning to Sydney, venue for the 2000 Olympics, on Friday.
South Korean capital Seoul, which staged the Games in 1988, will receive the flame on Monday.
The flame, lit from the sun's rays in Olympia on March 25, will travel to 33 cities in the five continents represented by the Olympic rings.
It returns to Greece on July 9 for a final home tour before lighting the cauldron at the Olympic stadium on August 13.
