Indonesian troops are reported to have opened fire when they landed on a beach west of the Papuan provincial capital, Jayapura.
Reports from the human rights group Elsham say people in Yongsu Separi village feld in terror and took refuge nearby.
The reports also say more soldiers were sent to the area in trucks.
Residents are quoted as saying the troops have been sent ot the area because of suspicions that the villagers are in contact with a leader of the separatist OPM movement.
Indonesia's national police chief says it is too early to know if the killers of two US teachers and an Indonesian near the Freeport mine were politically motivated or simply criminals.
Although other government officials have pointed to separatist rebels as the likely culprits, Da'i Bachtiar has said he cannot say whether this has any political nuances.
The military has blamed Papuan rebels for the killings but the rebels have denied any role in the incident.
The military's efforts to apprehend those involved in the shooting have so far been unsuccessful.
The US embassy has called the killings an act of terrorism.
Several US survivors of last Saturday's ambush are in medical care in Australia.
They are reportedly being protected by US police and have not spoken to the media about the attack.
