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.
President Donald Trump said on Friday the US was getting very close to meeting its objectives as it considers winding down its military efforts in the Iran war and called on countries that use the Strait of Hormuz to guard and police it "as necessary".
Iran is ready to let Japanese-related vessels pass through the Strait of Hormuz, a vital artery for global oil supplies, Kyodo news has reported, citing Iranian Foreign Minister Abbas Araqchi.
The Israeli military said early on Saturday it was striking Hezbollah targets in Beirut, after issuing an evacuation warning for seven neighbourhoods in the southern suburbs of the Lebanese capital.
The US military is deploying thousands of Marines to the Middle East, officials told Reuters on Friday, as President Donald Trump accused NATO allies of cowardice over their reluctance to send forces to help open the Strait of Hormuz.
A fire that broke out around lunchtime on Friday at a car parts factory in the South Korean city of Daejeon on Friday, has left 10 people dead, 25 seriously injured and 34 with minor injuries, the country's safety ministry said on Saturday.