Indonesia's military says the West Papua Liberation Army set fire to a digger owned by a state-owned construction company on Tuesday.
The attack on Istaka Karya's operations in Nduga regency follows the killing of at least 16 of its employees there by the Liberation Army in December. The Liberation Army has claimed the staff were actually Indonesian military in disguise.
In the aftermath of the massacre, hundreds of Indonesian military and police forces deployed to the area in a hunt for the armed group.
Military spokesman Colonel Muhammad Aidi said Liberation Army fighters burned an already-broken excavator in Yigi district and fired shots in the area.
He said when military soldiers arrived, the rebels fled without a gunfire exchange.
A spokesperson for the Liberation Army, Sebby Sambon, disputed this account, saying an unknown number of military and police were injured in a shootout which took place on Tuesday night and Wednesday morning.
However, he said he had only received an initial and unverified report from Liberation Army officials.
Mr Sambon said the battle took place after an ultimatum the Liberation Army gave to the military and police, which included demands that all non-Papuans leave Nduga and that Indonesia's flag be lowered across the regency.
In a statement, Liberation Army Commander Ekianus Kogeya said if the ultimatum was not complied with, there would be another attack.