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.
Iran and Israel targeted each other with missiles and airstrikes early on Saturday after Israel launched its biggest-ever air offensive against its longtime foe in a bid to prevent it from developing a nuclear weapon.
Israeli fire and airstrikes killed at least 35 Palestinians across the Gaza Strip, most of them near an aid distribution site operated by the US-backed Gaza Humanitarian Foundation, local health authorities said.
The death toll from the Air India plane crash in Ahmedabad rose to 270 on Saturday, as grieving families expressed frustration over delays in the release of victims' bodies, many of which were badly charred in the tragedy.
US President Donald Trump urged Iran on Friday to make a deal on its nuclear programme before it faced more attacks from Israel that he said would be "even more brutal."
Israel launched widescale strikes against Iran on Friday, saying it targeted nuclear facilities, ballistic missile factories and military commanders and that this was start of a prolonged operation to prevent Tehran from building an atomic weapon.