"We went to the site where Deputy Minister Illanes was and we found him lifeless. We are very shocked, we are running a risk because the miners are furious," Efe news agency quoted Flores as saying.
Flores told Erbol Radio by telephone from Panduro, some 180 kilometres from La Paz, where clashes erupted between miners and police.
Illanes was taken prisoner by miners as he tried to persuade them to end roadblocks and he had said earlier on Thursday that authorities need to establish a dialogue with the protesters.
"I am being held by the comrades, I have not received any mistreatment," Illanes has told a reporter earlier.
"I am in very good health, let my family be reassured. I am sitting in a place guarded by the comrades so people do not harm me," he said.
Illanes spoke from Panduro, where he travelled early on Thursday with the hope of convincing the miners to clear the roadblocks and enter talks with the government of President Evo Morales.
Instead, the miners took the deputy minister prisoner.
