Japan's western prefecture of Osaka confirmed a record daily total of 1,262 new coronavirus cases on Saturday, along with 41 deaths, national broadcaster NHK reported.
Osaka's previous high was 1,260 infections, announced on Wednesday, NHK said.
The capital Tokyo has also seen a surge in infections, with 1,050 new cases on Saturday, according to the broadcaster, after reporting in excess of 1,000 cases on Thursday as well.
The worsening situation has sharpened focus on whether the postponed Tokyo 2020 Olympic Games can or should go ahead, with the opening ceremony only 12 weeks away.
While Japan has avoided the kind of explosive outbreak of the virus seen in some other countries, the latest rise in infections has stoked alarm, with a surge in one variant and a critical shortage of medical staff and hospital beds in some areas.
Japan has also been slow with its vaccination drive, which kicked off in mid-February. Less than 2% of the population has been inoculated so far, the lowest proportion among wealthy countries.
In total, Saturday saw 3,212 new cases and 24 deaths across Japan, NHK reported.
The flare-up comes despite Osaka, Tokyo and two other prefectures having been placed since Sunday under states of emergency requiring the closure of bars, restaurants serving alcohol, department stores, cinemas and other commercial facilities larger than 1,000 square metres (1,200 square yards).
Japan's third state of emergency covers the "Golden Week" holiday in Japan when Japanese traditionally take vacations, thus dealing another blow to the tourism and services industries.