The current state of emergency in the capital and eight other metropolitan areas was to end next Monday, but hospitals in some areas are still overflowing with Covid-19 patients and serious cases have recently hit new highs.
The 20-day extension covers nine areas ranging from Hokkaido in the north to Fukuoka in the south. A 10th area, the southern island prefecture of Okinawa, is already under emergency status through June 20.
Olympic organisers must decide at about that time whether to allow any fans at all, after overseas spectators were banned months ago. A plan to prioritise vaccinations for Japanese athletes is expected to begin around then, according to media reports.
The Olympics are scheduled to start July 23 after a one-year postponement due to the pandemic, and worries about new variants and Japan's slow vaccination rollout have triggered calls from the public, medical experts and even a sponsor to cancel the games.
Suga's public support ratings have plunged to about 30 per cent from around 70 per cent when he took office in September.
Experts have warned that the variants are infecting more people, leaving them seriously ill and flooding hospitals in some areas.
Japan has lagged on vaccinations due to bureaucratic and planning missteps and shortages of medical staff. Only 2.3 per cent of the population has been fully vaccinated, and the current phase targeting older adults is not scheduled to finish before the games start.
Still, Suga and his government are determined to host the Olympics. The International Olympic Committee has also said the games will go ahead even if host city Tokyo is under emergency measures.
The government has been pushing to speed up inoculations and aims to administer up to 1 million a day, but some experts say that's an overly optimistic target.
Japan has reported about 730,000 coronavirus cases and more than 12,700 deaths.
