Heron Sixto Lopez, who ran a legal aid center for Mixtec and Triqui indigenous people in the town of Juxtaluapa, in the southern state of Oaxaca, was reported missing five days ago.
His bullet-riddled body was found on Saturday, Victor Alonso, a regional prosecutor, told AFP.
"He had at least six bullet wounds in different parts of his body," Alonso said.
Lopez's murder follows Wednesday's killing in Oaxaca of a 28-year-old crime reporter for the local newspaper El Imparcial.