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.
SpaceX's next-generation Starship rocket reached orbit for the first time on Monday despite having one of its engines shut down unexpectedly, overcoming a hitch mid-flight to deploy its first batch of new Starlink satellites in a truncated mission ending hours earlier than originally planned.
British police said on Monday they were investigating whether individuals acting for a foreign state were involved in an apparent plot to attack an airbase used by the United States but said five suspects they had arrested would be released on bail.
Thousands sheltered on Monday in evacuation centres in the Thai capital, parts of it still flooded after havoc brought by intense weekend rain, while swelling reservoirs in an eastern province triggered orders for more to leave their homes.
Heavy rain and storms have triggered floods and landslides that killed 56 people in India, while in Nepal, 14 have died and another 11 are missing, with authorities warning on Sunday that more flash floods are possible.