The three -- one security employee and two police officers on duty at the mine -- were on patrol at the huge Grasberg complex in Papua province before they were found dead late yesterday.
Police found deep gashes on the three bodies as well as bullet wounds on one of them, Papua police spokesman Patrick Renwarin said.
"We still don't know the cause of the deaths yet as we are still waiting for the full report," Renwarin said.
Pro-independence militants have waged a low-level insurgency against Indonesian rule in Papua, which is off-limits to foreign journalists without special permission.
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Grasberg, one of the biggest copper and gold mines in the world, has been plagued by accidents and production problems in recent years.
In May 2013, a training tunnel collapsed killing 28 miners as they took part in a safety course in one of Indonesia's worst-ever mining accidents.
In 2011 a three-month strike crippled production at the mine, and workers only halted the industrial action once Freeport agreed to a huge pay rise.