Tokyo, which will host the Olympic Games in less than four months, confirmed more than 500 new infections on Thursday for the second straight day, reports dpa news agency.
Japan adopted the measure in Osaka, Miyagi and Hyogo prefectures earlier this week.
It is expected to come into effect in Tokyo, Kyoto and Okinawa on April 12.
Under the semi-state of emergency, bars and restaurants are asked to close by 8 p.m. and attendance at large events is limited to 5,000 people.
The move comes just three weeks after the government lifted a state of emergency in Tokyo and its neighbouring three prefectures which had been imposed in early January.
The roll-out of Covid-19 vaccines has been extremely slow since its launch in mid-February. Only 0.3 per cent of the population has been fully vaccinated, according to the Ministry of Health, Labour and Welfare.
The western prefecture of Osaka declared a state of medical emergency on Wednesday as hospitals were overwhelmed by the pandemic.
Osaka reported 905 new cases on Thursday, marking the highest daily rise for the third day in a row.
The surge is attributed to more contagious variants of the coronavirus, Osaka Governor Hirofumi Yoshimura told a news conference.