The current emergency in the capital and eight other metropolitan areas was to end next Monday, but hospitals in some regions are still overflowing with Covid-19 patients.
There is a concern that lifting the emergency would cause an instant rebound in infections, economy revitalisation minister Yasutoshi Nishimura said.
Mr Nishimura told reporters the government proposal of a 20-day extension to June 20 in the nine areas received preliminary approval from experts ahead of an official announcement later on Friday.
The southern island prefecture of Okinawa is already under emergency status until June 20.
The Tokyo Olympics are scheduled to start on July 23 after the Games were delayed by a year due to the pandemic.
Olympic organisers have to yet to decide around whether domestic fans will be allowed, after overseas spectators were banned.
A plan to prioritise vaccinations for Japanese athletes has also been delayed, according to media reports.
Just 4% of the population has had at least one dose of a Covid vaccine and only 2.3% of the population has been fully vaccinated, while doctors in Osaka warned this week that hospitals were close to collapse.
Japan has lagged on vaccinations due to bureaucratic and planning missteps, along with shortages.
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Worries about new variants and Japan’s slow vaccination rollouts have triggered protests from the public and calls from medical experts to cancel the Games.
Experts have warned that more contagious variants are infecting more people, leaving them seriously ill and flooding hospitals.
Recent polls indicate that between 60-80% of people in Japan want the Games to be cancelled or postponed.
Doctors have been leading many of the protests as they have seen a rise in cases of the UK virus variant and fear the Indian strain will come next.
But Prime Minister Yoshihide Suga and his government are determined to host the Olympics.
The International Olympic Committee has also said the Olympics would go ahead even if the host city Tokyo is under emergency measures.
Japan has reported about 730,000 cases of infection and more than 12,700 deaths.