Tokyo on Wednesday reported 55 new coronavirus infections, the highest daily increase since early May.
According to the neighbouring prefecture of Saitama Local Government, 12 new cases were confirmed on Wednesday, also the largest since early May.
However, a coronavirus state of emergency ended in Tokyo, Saitama and three other prefectures in late May, the last remaining regions subject to restrictions.
According to a broadcaster NHK tally, Japan confirmed 18,755 cases, including 712 on a cruise ship quarantined near Tokyo in February, and 978 deaths.
Japan lifted its restrictions on cross-prefectural travel on Friday, though dozens of new coronavirus infections were reported daily.
Meanwhile, long-distance travellers returned to airports and train stations as the Federal Government officially stopped requesting people not to travel across prefectural borders.