Hugo Alvaro Gomez Vasquez, who is suspected of taking part in the weekend massacre in the northern province of Peten, is a former member of the kaibiles, Guatemalan soldiers trained in counterinsurgency methods, Colom said.
"The evidence indicates that he is a one of the high leaders of the Zetas," Guatemala's president told reporters. The Zetas are a brutal, Mexico-based drug cartel that has spread into northern Guatemala.
Gomez Vasquez was taken by helicopter to the capital 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 Peten."
Guatemalan authorities said 25 of the 27 victims in the weekend attack had been decapitated. Three survivors are helping authorities in their search for the culprits.