About 3,000 spectators were expected to attend the relay’s starting ceremony in Fukushima on March 25 but organisers have scaled back the event over Covid-19 concerns.
Officials announced the Olympic flame will be removed from display following the declaration of the state of emergency in Japan and the postponement of Olympics to 2021.
The flame arrived in Japan from Greece on March 20 and the torch relay was to have started last week from Fukushima. It has remained in the prefecture with Wednesday's "handover ceremony" merely symbolic.
The flame arrived in Japan to a scaled-down welcoming ceremony on Friday as doubts grew over whether the 2020 Tokyo Olympics will go ahead on schedule as the deadly virus causes chaos around the world.
The flame, carried in a burning canister, touched down amid growing doubts if the Tokyo Games can open as scheduled on July 24 because of the coronavirus pandemic.
The spread of COVID-19 has raised questions over whether this year's Olympic Games can go ahead as planned.
The torch will arrive in South Korea on November 1 for the start of the domestic torch relay of the Pyeongchang 2018 Winter Olympics.
Amputee swimmer who survived bombing in Syria runs with the Rio 2016 Olympic flame during the torch relay at the Eleonas refugee camp in Athens.
Syrian refugee athlete will carry the Olympic flame through Greek refugee camp
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