The 77-year-old emperor "will be hospitalised from tonight because he has had a persistent fever and begun to show more concerning symptoms of bronchitis," said a spokesman for the imperial household agency on Sunday.
The emperor will be treated at the University of Tokyo Hospital only days after his granddaughter Aiko -- the only child of Crown Prince Naruhito and Crown Princess Masako -- was hospitalised there for pneumonia.
Aiko was discharged on Saturday.
Akihito, who acceded to the throne in 1989 following the death of his father Emperor Hirohito, underwent surgery to remove prostate cancer in 2003.
As the titular head of state in Japan, he plays a largely ceremonial role but is held in deep respect by many Japanese.