Hugo Alvaro Gómez Vásquez is a former member of the Kaibiles, specialized soldiers trained in counterinsurgency tactics, Colom said.
Colom said Gómez Vásquez is suspected of taking part in the weekend killings in the northern province of Petén.
Gómez Vásquez was taken by helicopter to Petén's capital of Alta Verapaz under heavy security.
He denied the charges in a brief statement to the media, saying, "They are accusing me of many things ... but I'm a farmer. I'm from Petén."
Based on reporting by The Associated Press.