The executions allegedly were carried out by army staff overseen by Colonel Nelson Velazquez Parrado.
"The country's 40th local criminal court ... Has ordered the detention at the jail unit of Colonel Nelson Velazquez Parrado for the homicides of 15 people in Antioquia," a northern department, in 2007, the prosecutor's office said in a statement yesterday.
The colonel has been charged with manslaughter, as well as conspiracy, weapons charges and falsifying documents, it added.
Currently, some 20 other generals are under investigation for similar alleged offenses, according to prosecutors.
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More than 220,000 people have died in the Colombian conflict, which has involved drug traffickers and right-wing death squads, as well as government troops and leftist guerrillas.
Bogota and FARC rebels have been holding peace talks in the Cuban capital Havana for the past three years.
They have signed partial deals on several issues, but have yet to reach a definitive peace accord.
Founded in 1964, the Revolutionary Armed Forces of Colombia currently comprises an estimated 7,000 fighters.