Shigehito Kaga, 55 year-old-amateure bicyclist, said he would like to enjoy the Olympics held in his city as this could be his once in his lifetime experience.
Tokyo organizers and the IOC earlier in the week barred all fans from venues in Tokyo and three neighboring prefectures.
Local governor Naomichi Suzuki announced the move late Friday night, reversing a decision a day earlier by Olympic organisers allowed some fans at competitions held elsewhere.
The public was kept away from the arrival of the flame and a welcoming ceremony was attended only by the media and officials.
No alcohol at bars, curtailed timings for concerts and conferences: Japan announces virus emergency throughout Olympics
With just two weeks until the July 23 opening ceremony, coronavirus infections are rising in the capital, and the spread of the more infectious Delta variant has spooked officials.
The emergency measures -- less strict than a blanket lockdown -- will be in force until August 22, several Japanese media outlets reported, following a rise in cases.