It comes as violence continues to rock Papua and West Papua provinces, where dozens have died during clashes.
An official with the country's social ministry said the air force has flown around 7,500 people out of Wamena after unrest there in the past month.
Reuters reports Harry Hikmat saying another group of nearly 4,200 residents left on commercial flights.
A police spokesperson said the situation in Wamena is now stable, with shops and markets again open.
Meanwhile, several Indonesian government ministers are expected to visit to Wamena today.
Antara reports they are to outline steps for the "comprehensive restoration of security and stability".
The Coordinating Minister for Political, Legal, and Security Affairs, Wiranto, is leading a delegation of several ministers to the Highlands city.
These include Social Affairs Minister Agus Gumiwang Kartasasmita, Health Minister Nila Moeloek, State Enterprises Minister Rini Soemarno, and Public Works and Housing Minister Basuki Hadimuljono will also visit Wamena.
Accompanying them will be the heads of Indonesia's military and police forces, Marshal Hadi Tjahjanto and General Tito Karnavian.
Despite the evacuations, Mr Tjahjanto said the consensus among most native Papuans was that non-native Papuan residents should continue to stay in Wamena, as well as other Highlands towns in the region, including Ilaga and Oksibil.
According to Antara, following the unrest in Wamena, thousands of residents, mostly non-Papuans, have sought temporary shelter in local military and police compounds.
The news agency reports that due to the unrest in Wamena on 23 September, 33 people were killed, while at least 77 others sustained injuries in the riot which destroyed much of the town.
Source: RNZ
