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 until June 20.
The state of emergency in the capital and eight other metropolitan areas was scheduled to end on May 31 but cases remain high and medical systems are still overburdened, prime minister Yoshihide Suga said in announcing the decision.
Earlier this month, the Tokyo Medical Practitioners Association stressed that hospitals in the Games host city, Tokyo, “have their hands full and have almost no spare capacity” amid a spike in infections.
But Mr Suga and his government remain 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.
Japan has so far reported about 730,000 coronavirus cases and more than 12,700 deaths while its vaccination programme has lagged due to bureaucratic missteps and shortages, reported the Associated Press.
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 in July, the agency added.
Foreign spectators were banned from travelling to watch the games months ago but the president of the organising committee hinted on Friday that even local fans may be barred from venues.
Seiko Hashimoto said: “We would like to make a decision as soon as possible (on fans), but after the state of emergency is lifted we will assess.
“There are many people who are saying that for the Olympic Games we have to run without spectators, although other sports are accepting spectators,” she added. “So we need to keep that in mind. We need to avoid that the local medical services are affected. We need to take those things into consideration before agreeing on the spectator count.”