Some 20 human rights organizations called an emergency meeting in the capital to discuss the incident and called for a protest in front of the presidential palace.
"We've been saying for a long time that the army's use of force brings with it the risk that something like this could happen," said Francisco Soto, a representative of the Center for Legal Action and Human Rights.
Six of the dead were buried Friday afternoon in Totonicapan, where thousands gathered to watch their coffins pass through the town's central square. Hundreds shouted "Justice! Justice!" while dozens of mourners hurled themselves toward the coffins in grief.
Thursday's protest was fueled by anger at Perez Molina, who has proposed constitutional reforms that he says will modernize Guatemala's economic and regulatory systems.
Among other changes, the reforms would set price caps on electricity, and require teachers to get a five-year bachelor's degree instead of a three-year vocational degree.
The protesters think the price caps are too high, and object to the longer process for obtaining a degree that many in the subsistence-farming area depend on to improve their livelihoods.
In a protest in May, about 200 people armed with machetes and guns briefly seized an army outpost in a province bordering Mexico to demand justice for the killing of a man who opposed the construction of a hydroelectric plant. Perez Molina responded by declaring a state of siege in the area and granting the army emergency powers.
Associated Press writer Moises Castillo reported this story in Totonicapan and Romina Ruiz-Goiriena reported from Guatemala City.