The trio had been brought in as part of efforts to keep up production at the giant Grasberg complex, which is owned by Freeport McMoRan and is one of the world's biggest gold and copper mines.
Police from the Mimika district in Indonesia's restive Papua province said two bodies were recovered Friday from a burning Freeport-owned car on a road to the mine, and the third nearby.
"The three men were found dead yesterday and are yet to be identified. Today we will continue to investigate who the attackers might be and how the shooting happened," Mimika police spokesman Mada Laksanta told AFP.
"Two military officers and a Freeport security guard were also shot. The officers were shot in the leg and the guards in the right arm."
More than 8,000 of Freeport's 23,000 workers at the mine, near the town of Timika, have been on strike since September 15, demanding significant wage increases.
The dispute, coupled with strikes at Freeport's South American mines, has raised concerns of a copper shortage, but analysts say any impact could be limited by falling demand for the metal.
Protests turned violent Monday when strikers clashed with police, who shot dead one worker and injured at least six others. Striking workers have since blocked the only road to the mine.
The strikers, mostly indigenous Melanesians, say they are the lowest paid Freeport workers in the world, earning between $1.50 and $3.50 an hour.
They are demanding their wages go up more than eightfold to a minimum of $12.50 an hour and a maximum of $32. The company's offers now stand at around 25 per cent.
Freeport's Indonesian unit said the ambush took place in the same area as a fatal shooting on April 7.
"We are deeply saddened by the loss of lives of our fellow co-workers and our condolences go out to their families," Freeport Indonesia spokesman Ramdani Sirait said.