The restrictions are being imposed in areas surrounding the capital as well as in the city of Osaka.
Japan has had some success fighting Covid-19 but is now seeing record cases fuelled by the virulent Delta strain.
Daily cases nationwide topped 10,000 for the first time on Thursday, more than a third of them in the capital.
Tokyo – where the Olympics are mainly taking place – has seen three straight days of record cases and logged another 3,300 on Friday, even though it is already under a state of emergency.
More than 60% of the city’s hospital beds available for serious cases have been filled.
Olympic organisers reported 27 new cases at the Games on Friday, bringing the total since the start of July to more than 200. But with strict rules in place, including a ban on spectators, organisers deny the event is driving the rise in cases.
Despite this, some experts worry that holding the Olympics in such circumstances sends a confusing message to the
Japan’s Health Minister, Norihisa Tamura warned that the country had entered a new, “extremely frightening”, stage of the pandemic.
Under the state of emergency, bars and restaurants must stop serving alcohol and close early.
Three regions, known in Japan as prefectures, along with Osaka, will go under the restrictions from 2-31 August, with the measures in place in Tokyo are being extended to the end of the month.
Tokyo’s Governor Yuriko Koike has said the key to controlling the outbreak is young people, urging them to get vaccinated, but the BBC’s Mariko Oi says this is a little unfair given the low availability of doses.
Speaking to the BBC, some young Japanese people were sceptical about whether the new measures would work.
“If the government really wants to stop the spread of the virus, they have to lock us down and offer financial support,” said another.