The body of Luis Francisco Cuellar of Caqueta state was found from Florencia, security official Edilberto Ramon Endo said.
Cuellar's wife, Himeldo Galindo, also confirmed the death, but was too distraught to offer details.
The governor was kidnapped by eight to 10 men in military uniforms who arrived at his home late Monday, Dec 21.
Colombian President Alvaro Uribe earlier on Tuesday, Dec 22, launched a massive operation to find and rescue the missing governor.
Defense Minister Gabriel Silva blamed the kidnapping on the FARC unit and announced a $500,000 reward for information leading to Cuellar's rescue.
Cuellar already was kidnapped for ransom four times since 1987.