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.
Israel and Iran attacked each other for a fifth straight day on Tuesday, and US President Donald Trump urged Iranians to evacuate Tehran, citing what he said was the country's rejection of a deal to curb nuclear weapons development.
Israeli tank shellfire killed at least 51 Palestinians on Tuesday as they awaited aid trucks in Khan Younis in the southern Gaza Strip, the territory's health ministry said, adding that dozens of others were wounded.
Russia launched hundreds of drones and dozens of missilesat Ukraine on Tuesday,hitting dozens of civilian targets in Kyiv including a large apartment block, killing at least 15 people and wounding scores, Ukrainian officials said.
US President Donald Trump left the Group of Seven summit in Canada a day early due to the situation in the Middle East, the White House said on Monday.
The U.S. military has moved a large number of refueling aircraft to Europe to provide options to President Donald Trump as Middle East tensions erupt into conflict between Iran and Israel, two U.S. officials told Reuters on Monday, speaking on condition of anonymity.