The 78-year-old, who has suffered from poor health recently, will spend five hours in surgery at the University of Tokyo Hospital.
A spokesperson said doctors had decided to carry out the operation after conducting test earlier this month, and the procedure would serve to "maintain and to improve his majesty's daily life".
The Japanese head of state – pictured greeting doctors with his wife Empress Michiko – ascended to the throne in 1989 following the death of his father, Emperor Hirohito.
According to Japan's Imperial House law, the emperor is succeeded on his death by the nearest male relative. This would be Crown Prince Naruhito.
The emperor's second son, Prince Akishino, called for debate on the law to allow for a retirement age for his father.
Akihito spent three weeks in hospital last November, suffering from bronchitis.
He also suffered stress-related health issues in late 2008 and had surgery for prostate cancer in 2003.