Of the 206 Japenese nationals evacuated from the Chinese city of Wuhan, four have been reported ill.
They will now undergo medical checks at a hospital designated for infectious diseases.
The remaining passengers will also under health checks before they are allowed to go home, officials added.
The first chartered flight from Wuhan, where the coronavirus was first detected, arrived in Tokyo on Wednesday.
So far, Japan has confirmed seven cases.
The death toll from the coronavirus, believed to have originated in a Wuhan market which illegally sold wildlife, rose sharply to 132 on Wednesday, with nearly 1,500 new cases.
Meanwhile, efforts are on to evacuate another 650 Japanese citizens, with Prime Minister Shinzo Abe setting up a special task force to deal with the epidemic.
Cardinals are scheduled to meet on Tuesday to plan Pope Francis' funeral, which leaders from around the world will attend ahead of a conclave next month to elect a new head of the Roman Catholic Church.
Russian President Vladimir Putin proposed on Monday bilateral talks with Ukraine for the first time since the early days of the war, and his Ukrainian counterpart Volodymyr Zelenskyy said Kyiv was eager to discuss a halt to attacks on civilian targets.
Ukraine issued air raid alerts for Kyiv and the country's eastern half as blasts shook the city of Mykolaiv early on Monday, authorities said, hours after the one-day Easter ceasefire declared by Russian President Vladimir Putin came to an end.
US Vice President JD Vance began a four-day visit to India on Monday and will hold talks with Prime Minister Narendra Modi, as New Delhi rushes to avoid steep US tariffs with an early trade deal and boost ties with the Trump administration.