Ishinosuke Uwano, 83, was officially registered as dead by the Japanese government in 2000, as he had not been heard from since 1958 when he was last reported seen on Russia's Sakhalin Island.
It was unclear why and how Uwano, who served in the Japanese Imperial Army on Sakhalin until the war's end in 1945, ended up in Ukraine.
Shortly after arriving at Tokyo's Narita international airport, Uwano told reporters in Russian: "I have never spoken Japanese for 60 years, and first of all I would like to say to you 'konnichiwa', (good afternoon).
"I'm looking forward to seeing and talking with my brothers and cousins."
He was drafted into the Japanese Imperial Army in 1943 to join other soldiers on Sakhalin Island.
Japanese media said Uwano moved to Ukraine in 1965 and married a Ukrainian woman. Uwano, who has three children, lives in Zhitomyr, west of the Ukrainian capital of Kiev.
During a 10-day visit to Japan, Uwano plans to travel to his home in Iwate, about 450 km north of Tokyo, to see relatives and friends and visit the graves of his parents.
Since finding Uwano in Ukraine in October, Japan's health ministry has been trying to restore his residency registration.
"He is visiting Japan as a foreigner this time. We are trying to restore his family register so that he can be confirmed legally as Japanese citizen," a Health Ministry official said.
Uwano has Ukrainian nationality.