Government minister Carlos Romero called it a "cowardly and brutal killing" and asked the miners to hand over the body of deputy minister Rodolfo Illanes.
Earlier, Mr Romero said that Illanes had been kidnapped and possibly tortured.
But now Mr Romero and Reymi Ferreira, defence minister, can confirm that the vice minister of government had been beaten to death by the miners, who are demanding more rights, including the right to associate with private companies.
Illanes had gone to Panduro, a town 80m (130km) south of the La Paz, where the strikers have barricaded a highway since Monday, to open discussions.
Protesters have been demanding more mining concessions, the right to work for private companies, and greater union representation.