The coronavirus measures will remain in place throughout the Tokyo Olympics, with businesses selling alcohol being asked to shut to stop people from drinking and partying.
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Tokyo has entered another state of emergency, which will last through the duration of the upcoming Olympic Games.
The measures, mainly targeted at preventing the sale of alcohol, came into force on Monday, less than two weeks from the start of the games.
It is the fourth state of emergency in the Japanese capital since the start of the COVID-19 pandemic, and is intended to stop people from getting drunk and partying while the Olympics are on.
International spectators had long been banned from attending the games, and on the weekend organisers decided to bar local spectators from events in Tokyo and other areas too, as the city deals with a surge in coronavirus cases.
They make up the overwhelming majority of Olympic venues, although a smattering of outlying areas were allowed initially to have limited attendance.
Now, two prefectures that were permitted to have fans have backed out of those plans.
Fukushima prefecture in northeastern Japan has decided to hold its baseball and softball events without spectators.
It has been joined by the northern prefecture of Hokkaido, which will hold soccer games without fans at the Sapporo Dome.
The main focus of the emergency is a request for bars, restaurants and karaoke parlours serving alcohol to close.
A ban on serving alcohol is a key step to tone down Olympic-related festivities and to stop people from drinking and partying.
Tokyo residents are expected to face stay-at-home requests and watch the games on TV.
The opening ceremony will take place on July 23.