New coronavirus infections in Tokyo hit a record high of more than 1,300 on Thursday raising fears of an explosion in cases, local media reported, and New Year's Eve celebrations were curtailed as the country battles a third wave of the pandemic.
Scores of flights were also cancelled as heavy snowfall hit several areas of Japan on Thursday.
Japanese Prime Minister Yoshihide Suga has urged people to celebrate New Year quietly, and avoid non-essential outings, amid the twin crises.
Japan Airlines and All Nippon Airways cancelled or planned to cancel a total of around 140 flights, public broadcaster NHK reported, adding that a bullet train had suspended services in some parts of the northern Yamagata prefecture.
A 70-year-old man died in the northern Iwate prefecture after he apparently fell into a river while trying to shift snow with a shovel loader machine, NHK said.
Japan has been battling the third wave of Covid-19 infections in recent weeks and on Monday started barring the entry of non-resident foreign nationals after detecting variants of the virus from Britain and South Africa.
Japanese Economy Minister Yasutoshi Nishimura said on Wednesday the government may have to consider declaring a state of emergency if the number the Covid-19 cases grow.
Japan's Imperial Household Agency has cancelled an annual New Year's event set for Jan. 2, at which Emperor Naruhito and other imperial family members were due to greet well-wishers.
People have been asked to stagger visits to shrines, traditionally popular destinations over New Year's Eve and New Year's Day.
In Tokyo, where the governor has warned of a potential explosion in Covid-19 cases amid record daily increases, extra train services will be suspended from late Dec. 31 to Jan. 1.
"I want to emphasize again that there are no New Year holidays for the coronavirus. I urge people to spend quiet holidays staying at home with families," Kyodo news agency quoted Tokyo Governor Yuriko Koike as telling reporters on Thursday.
Prime minister Suga will meet relevant ministers including Health Minister Norihisa Tamura and Economy Minister Nishimura later on Thursday to discuss Tokyo's coronavirus situation, local media said.
About 3,400 people have died in Japan from around 231,000 cases during the pandemic so far.