The Olympic flame arrived in Tokyo on Friday but with the public kept away at a low-key welcoming ceremony because of coronavirus fears, the day after a "heartbreaking" announcement that spectators would be banned from most Games events.

On a rainy morning exactly two weeks before the opening ceremony of the biggest sporting event since the pandemic began, the flame was brought on stage in a lantern and handed to Tokyo Governor Yuriko Koike.

Tokyo 2020 organisers and government officials on Thursday night announced their decision to bar fans from Olympic events in the capital, which will be under a virus emergency throughout the Games.

It means the pandemic-postponed Games will be the first to take place largely behind closed doors. A handful of competitions will take place outside the capital.

The torch relay was meant to build excitement for the Games, but it has been pulled from public roads in the capital to prevent crowds spreading the virus as infections rise.

Before the flame arrived, five male trumpet players dressed in suits played a rousing melody under a gazebo to shelter them from the drizzle, in front of only journalists and a handful of officials.

The stands stood empty at the Komazawa Olympic Park stadium in the capital's southeastern suburbs, which was used in the 1964 Tokyo Olympics.

"I'm glad that we welcome the torch relay, with these legacies we proudly show at home and abroad," Koike said.

But the Tokyo governor, who was recently hospitalised for exhaustion, coughed three times during her brief speech and several more times after that.

Friday's event gave a taste of the atmosphere that could await athletes at the opening ceremony, to be held at the National Stadium in the city centre.

The decision to bar fans came after the government said a state of emergency would be imposed in Tokyo throughout the Games to curb a rebound in infections and fears over the more infectious Delta variant.

On Thursday night, Koike could not hide her disappointment at having to no fans at the Games.

"I feel heartbreaking grief about this decision," she said.

When the 2020 Games were postponed last year as the scale of the pandemic became clear, there was talk they would be staged as proof the world had overcome the virus.

But that triumphant tone has given way to the harsh reality of new infection surges and more contagious variants, including the Delta strain that has led to virus resurgences in many countries.

The nationwide torch relay has been fraught with problems since it began in March, with almost half the legs disrupted in some way.

The relay was forced off public roads in famous tourist cities such as Kyoto and Hiroshima over fears that crowds of fans could spread the virus.

And it has also met with some public opposition, with a 53-year-old woman arrested on Sunday for squirting liquid from a water pistol towards a runner.