There were a record 1,337 cases in Tokyo on December 31, with 783 new infections announced on new year's day.
Tokyo 2020 organisers have previously stated their hopes that all athletes, and potentially spectators too, can be vaccinated against Covid-19 by July, but host towns for preparation camps have expressed less optimism.
Costs for the Games have increased by $NZ3.97b because of measures needed to prevent the spread of coronavirus, which could make them the most expensive summer edition in history.
A poll by national broadcaster NHK showed that the majority of the Japanese public oppose holding the Games in 2021, favouring a further delay or outright cancellation of the event.
Last week, the Japanese government started banning the entry of non-resident foreign nationals following the discovery of the UK variant.
Tokyo 2020 is expected to update athletes and spectators next week on preparations for the Games as it marks 200 days until the July 23 Olympics.
Japan has recorded 239,041 coronavirus cases and 3,337 deaths during the pandemic, according to Johns Hopkins University.
The president of the International Olympic Committee also underlined the organisation's "determination" to stage Tokyo 2020 as planned and claimed the Olympic Movement had "strengthened the role of sport in society" during the coronavirus crisis.
"Tokyo is still the best-prepared Olympic city ever," Thomas Bach said in a video address to mark the start of 2021.
"We can only thank our Japanese partners and friends for their great commitment and their determination, which is absolutely in line with our commitment and our determination to organise these Games in a safe and secure way for all the participants and to make these Olympic Games fit for the post-coronavirus world.
"We all will live unforgettable Games. These Olympic Games will be the light at the end of the tunnel. They will be a celebration of solidarity, of unity of humankind in all our diversity, and of resilience."
