Muramatsu, vice president of the Colombian subsidiary of Japanese industrial group Yazaki Corporation, was kidnapped by rebels of the Revolutionary Armed Forces of Colombia (FARC).
They demanded $27 million for his release. Armed Forces Commander General Carlos Alberto Ospina said late on Monday that the body was found in a mountainous area near the town of San Juan de Rioseco, 70 kilometers west of Bogota.
The body was positively identified on Tuesday, when investigators that traveled to San Juan cross checked the remains with Muramatsu's fingerprints and dental records.
Muramatsu's body was taken late on Tuesday to Bogota's National Institute of Legal Medicine for an autopsy.
Blaming the rebels
The deceased was dressed in an army camouflage uniform and had been shot with a rifle several times, Ospina said, adding that the guerrillas apparently murdered him when troops in the area came close to them.
Military officials blame a top FARC official, Jorge Briceno, also known as "Mono Jojoy", for Muramatsu's abduction.
Muramatsu's body was found 70
kilometres west of Bogota
The Yazaki subsidiary withdrew the only other Japanese executive in Colombia, the president, after Muramatsu's kidnapping and the 1100 workforce is now entirely composed of local staff.
On average some 3000 people a year are kidnapped in Colombia, most of them by leftist FARC rebels or a smaller guerrilla group, the National Liberation Army (ELN).
More than 200,000 people have been killed in Colombia's four
decade-long civil war.