Forty miners have been detained in the case.
Illanes was kidnapped and beaten to death by striking mine workers on Thursday after to going to the town of Panduro, 80 miles (130 kilometers) south of La Paz, to mediate in the dispute over mining laws and dwindling paychecks.
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The striking miners had armed themselves with dynamite and seized several highways, stranding thousands of vehicles and passengers.
Bolivia's Attorney General's Office has detained 40 miners, among them protest leader Carlos Mamani, president of the National Federation of Mining Cooperatives of Bolivia.
Yesterday afternoon, Mamani and two other federation officials were accused by the Public Ministry in Illanes' death.
An autopsy found that Illanes died from trauma to the brain and thorax.
The blockaded highway in Panduro was clear on Friday as the miners returned to their camps. A funeral Mass was held for Illanes in La Paz.
Illanes' murder underscored how President Evo Morales, a former coca growers' union leader, has increasingly found himself at odds with the same kind of popular social movements that fueled his rise to power and have made up his political base.
The leftist president called the beating death of the deputy minister "a conspiracy" to overthrow him.
Bolivia's informal miners number about 100,000 and work in self-managed cooperatives producing primarily zinc, tin, silver and gold.
They want to be able to associate with private companies, which promise to put more cash in their pockets, but are currently prohibited from doing so. The government argues that if they associate with multinational companies they will no longer be cooperatives.
Bolivia has seen increased social agitation as a financial slowdown hit an economy heavily dependent on natural gas and minerals, which account for over 70 percent of foreign export sales.
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