SORONG, Indonesia—Mile by mile, a ribbon of concrete is slicing through the mountains and dense forests that make up some of the world’s most inaccessible wilderness.

The Trans-Papua Highway is intended to connect ports in western New Guinea with the highland interior, a largely untapped area for timber and palm-oil companies. But the road’s construction is spurring violent resistance from Papuan separatists who fear it will lead non-Papuans to exploit and destroy the rain forest they rely on. On Thursday, three Indonesian...