While the incident has yet to be confirmed official, the story has been run on local media quoting Moises Flores, the director of a mining radio station.
"We have been able to see close up that vice-minister Illanes was dead. Colleagues told us that he had died of a beating," Flores said.
A subsequent autopsy found Illanes had died from trauma to the brain and thorax.
Illanes had been kidnapped earlier on Thursday after travelling to Panduro to talk with protesters.
Forty miners have been detained since the incident including Carlos Mamani, president of the National Federation of Mining Cooperatives of Bolivia. Mamani and two other officials have been charged with Illanes' death.
This tragedy occurred despite the Federation releasing a radio statement soon after the kidnapping saying the minister had not been harmed.
The protesters were protesting after a series of failed negotiations in which they demanded more mining concessions, the right to work for private enterprise, greater union representation, and the elimination of certain environmental regulations.
The strike turned violent on Wednesday when protesters blockaded a highway. Subsequent police clashes left three protesters dead and 17 police officers wounded.
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Bolivian Deputy Interior Minister Rodolfo Illanes has reportedly been ‘beaten to death’ by striking miners after being kidnapped.