Higher confirmed numbers were reported in all 47 prefectures, with infections more than doubling in Tokyo, Osaka and Kanagawa prefectures compared to the previous week, Xinhua news agency reported.
The resurgence was likely caused by a new Omicron sub-variant, fueling fears over the onset of the seventh wave of infections.
Tokyo reported 8,341 new cases on Wednesday, compared with 3,803 on the same day last week, according to the metropolitan government. The capital city confirmed 5,302 new cases on Tuesday.
In Tokyo, the seven-day rolling average of new cases amounted to 4,426.6 per day, up 86.8 per cent compared to the previous week.
Osaka and Kanagawa confirmed 4,621 and 3,038 new daily cases on Wednesday, respectively, bringing the nationwide tally of new daily Covid-19 infections to 45,821.
Fukuoka Prefecture in southwestern Japan reported 2,366 new cases, prompting the prefectural government to issue an alert and urge residents to take anti-virus measures.
Although Covid-19 infections declined across the nation since mid-May, they began to increase sharply in stages starting in late June, with newly confirmed cases exceeding 30,000 on Tuesday, as the BA.5 sub-variant began to spread and comprised an increasing share of the daily confirmed cases.