The relay began in north-eastern Fukushima prefecture, the area that was devastated by the 2011 earthquake, tsunami and the meltdown of three nuclear reactors.
The first runner with the torch was Azusa Iwashimizu, a key player in the Japanese football team that won the Women’s World Cup in 2011.
Wearing a white tracksuit, she carried the torch out of the J-Village indoor football training centre and was surrounded by 14 other members of the 2011 World Cup squad and coach Norio Sasaki at the rear.
The ceremony was closed to the public to limit any further spread of Covid-19 but was streamed live.
"The torch of Tokyo 2020 will become a bright light for hope for Japanese citizens and citizens in the world and a light at the end of the tunnel," said Seiko Hashimoto, former Olympian and Tokyo 2020 president.
Homare Sawa, the biggest star on the 2011 team, missed the ceremony. She is currently being treated for a condition affecting her inner ear and had to withdraw from the event.
Fans were told to socially distance along the roadside as the torch passes, and to refrain from loud cheering.
Organisers have said they will stop or reroute the relay if crowding becomes a problem during the four-month parade.
Spectators co-operated in Naraha Town, just down the road from where the torch started its trip. A few hundred people stood on the roadside and were safely spread out.
"At first I didn’t think much of it," said 20-year-old Takumu Kimura. "But when I actually saw it, it felt like, yes, it’s the Olympics."
Setsuko Hashimoto, a 63-year-old local resident, was emotional as the torch passed.
She said: "Ten years ago there was a nuclear accident so (seeing the torch) it felt like I could really look forward to something and live.
"When you become my age, this is the last Tokyo Olympics and it’s here. It was very touching," she added.
Prime minister Yoshihide Suga told reporters: "The Olympic torch relay starting from today is a valuable opportunity for the people to get a real sense of the Olympics and Paralympics that are approaching."
Just like past Olympics, the flame in the torch was blown out during one leg of the relay.
It was re-lit with a back-up lantern that also carries the flame that was kindled in Greece more than a year ago.
Sentiments expressed in polls in Japan so far are overwhelmingly negative, with about 80% suggesting another delay or cancellation.
The relay and the Olympics both stir further fear that the events could spread the virus, and there is also opposition to the soaring cost of staging the Olympics, now put officially at more than £11 billion, although several audits suggest it is twice that much.
About 10,000 runners are expected to take part, with the relay touching Japan’s 47 prefectures.
After the postponement a year ago, there was early talk of eliminating the relay to save money, but that idea was quickly dropped with the relay heavily sponsored by Coca-Cola and Toyota.
The relay is a prelude to the difficulties the Olympics and Paralympics will present with 15,400 athletes entering Japan, along with thousands of other officials, judges, VIPs, media and broadcasters.
Athletes will be kept in a bubble-like atmosphere in Tokyo and will be limited to the Athletes Village on Tokyo Bay, the competition venues and training areas. Most others will be outside the bubble and will be kept at a distance from the athletes.