The report said his family Sunday confirmed it was the cartoonist and quoted police as saying he may have fallen from a climbing path.
It added there was no sign of a suicide note.
Usui had been missing since September 11 after telling his family at his home in Saitama prefecture, near Tokyo, that he would be hiking on the mountain and would be back by the evening.
When he failed to return his family contacted police.
Usui made his debut as a manga author in 1987 and gained popularity in the 1990s with "Crayon Shin-chan" featuring the daily life of Shinnosuke, a mischievous five-year-old boy.