One of the three, a man in his 40s who had symptoms such as fever and coughing, first tested negative for coronavirus, the ministry said. But the man, who was initially diagnosed with pneumonia, later confirmed positive for the virus with an additional test, it said.
A Japanese government official who was handling accommodations for returnees from Wuhan was found dead at one of the facilities, and his death seen as a possible suicide, Japanese media reported on Sunday, amid criticism of government handling of the coronavirus.
Local police confirmed the death of a man but declined to comment on details as they were still investigating.
The government plans to send another chartered plane mid-week or later to bring back Japanese nationals who are still in China's Hubei province and its capital Wuhan, where the disease is thought to have originated, the foreign ministry said on Sunday.
Japan has emailed its citizens in the province to tell them of its plan, and is negotiating with China about Chinese spouses of Japanese citizens who also wish to travel to Japan, it said.
China is facing mounting isolation amid increasing international travel curbs and flight suspensions as the death toll from the coronavirus outbreak rose to 259.
The policy chief of Japan's ruling Liberal Democratic Party (LDP) said on Sunday that the coronavirus outbreak is affecting the nation's economy.
"It will surely have impacts on the economy. It is already impacting it by causing many cancellations in the tourism industry," Fumio Kishida, LDP's policy chief, said in a program carried by public broadcaster NHK.
Japanese Prime Minister Shinzo Abe has made tourism a key part of his economic policy, with a large proportion of foreign visitors from China, and major Japanese companies have factories in China.
Kishida also said the nation needed to develop rapid diagnostic test kits for the coronavirus, which could help with treatment.
Japan on Saturday moved to contain the economic impact of the outbreak as strict new measures aimed at limiting the spread of the virus came into effect.