The route for the relay, scheduled to start on March 26, 2020, was approved by the Japanese organising committee at a meeting with government officials.
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The torch will head south to the subtropical island of Okinawa - starting point for the 1964 Tokyo Games relay - before returning north and arriving in the Japanese capital on July 10, according to organisers.
"It is very significant to carry the torch of reconstruction across the country, beginning in Fukushima," said Tokyo governor Yuriko Koike.
Fukushima suffered heavily in the massive March 2011 tsunami, which slammed into a nuclear plant and triggered a meltdown of three reactors.
More than 18,000 people died in northeast Japan as a result of the huge earthquake and tsunami, while tens of thousands have been unable to return to their home towns.
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"By naming Fukushima as the starting point of the torch relay, it marks these Olympics as the Games of recovery," Masayoshi Yoshino, Japan's disaster reconstruction minister, told local media.
"We would like to see survivors take part as torch runners to help people in the disaster-hit areas."
The torch will visit all 47 Japanese prefectures before the lighting of the Olympic cauldron when the 2020 Games open on July 24.
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