Rodolfo Illanes and his bodyguard were seized earlier on Thursday at a roadblock in Panduro, south of La Paz, official said.
Interior Minister Carlos Romero said "all indications" were that Mr Illanes had been murdered in a "cowardly and brutal" attack.
Two miners also died from gunshot wounds during clashes with police.
Mr Illanes was beaten to death at about 18:00 local time (00:00 GMT), La Razon newspaper quoted Defence Minister Reymi Ferreira as saying.
The authorities could not for the moment retrieve his body, the minister said. More than 100 arrests had been made, he said.
President Evo Morales had been "profoundly affected" by Mr Illanes's death, Mr Ferreira added.
While he was being held, Mr Illanes told Bolivian radio that a condition for his release was that the government negotiate with miners over new legislation.
The miners have been blocking a highway in Panduro since Tuesday.
The National Federation of Mining Co-operatives of Bolivia, once strong allies of President Morales, began what they said would be an indefinite protest after negotiations failed.
Protesters have been demanding more mining concessions, the right to work for private companies, and greater union representation.
The Bolivian government says its deputy interior minister has been kidnapped and killed by striking miners.