Police arrested 73-year-old Yoshitane Yamasaki on suspicion of imprisoning his son, now aged 42, at their house in the city of Sanda in Hyogo prefecture, a local police spokesman told AFP.
Further details of the case were not available as the investigation is still underway, the spokesman said.
According to local media reports, the son was forced to live inside a wooden cage -- one metre (3.3 feet) high and 1.8 metre wide -- built in a prefabricated hut next to the main house.
The suspect has reportedly admitted the allegations.
The father said he fed his son and let him bathe every other day.
The son, whose name has been withheld, is in a stable condition but is suffering from a bent back, NHK said, adding that he was sent to a welfare facility.
(Except for the headline, this story has not been edited by NDTV staff and is published from a syndicated feed.)