Another variant was also detected in four people arriving from Brazil this week.
As many as 2,98,172 people have been infected in Japan till now with 4,539 people testing positive on Tuesday.
"But it's a great message to the world, as overcoming the battle against COVID".
Fewer people than in a normal year walk in Kyoto, western Japan, on January 13, 2021, amid the coronavirus pandemic.
At least 44 players and staff have nowtested positive to COVID-19.
The special treatment will be halted until Feb 7, the last day of an ongoing state of emergency in the Tokyo metropolitan area and some other parts of Japan, Suga said at a press conference.
"The emergency was just declared and what we should focus on is to make sure that restaurants are abiding by the request to operate until 8 p.m.", he said.
Restaurants and bars are already entitled to receive up to 60,000 yen per day if they comply with the request to shorten opening hours.
Record numbers of restaurants declared bankruptcy in Japan in 2020, according to Tokyo Shoko Research, eclipsing the previous high caused by the March 2011 quake and tsunami.
Despite the current surge in infections, Japan has reported far fewer infections than many countries of its size.
"We continue to see a serious situation", Prime Minister Yoshihide Suga said, adding that the measures were "indispensable".
Record infections and the threat of collapse of the hospital system eventually forced his hand.
It will mean about 55 per cent of Japan's population will be under restrictions.
Is the state of emergency response too late?
In an effort to help the struggling services sector, the Government had previously encouraged citizens to travel domestically and dine out by offering generous subsidies.
But it had to hit pause on the program late previous year as COVID-19 cases soared.
The emergency declaration, covering 55% of Japan's population of 126 million, is set to last through February 7 and is much narrower in scope than the first one last spring.
Suga eventually took action after calls from the local leaders, while his support ratings nosedived in polls showing the public increasingly dissatisfied with his handling of the virus.
The latest emergency declaration, however, is much narrower in scope than the first one last spring.
The measures come just over six months before the virus-postponed Tokyo Olympics are due to open.