Pilot Nay Linn Aung from Myanmar and his Indonesian co-pilot Makmur Susilo were killed along with eight passengers when their PC-6 Pilatus Porter aircraft crashed into the slopes of Mount Gergaji on Friday.
The aircraft had been in operation only seven months since it was bought from Switzerland.
The bodies were evacuated at 11 a.m. local time (9 a.m. Jakarta time) on board a Trigana Air plane from Ilaga to Moses Kilangin International Airport in Timika.
A medical team and officers from the Papua Police then conducted an identification of the bodies.
"I went to Ilaga this morning on board the Trigana Air plane to get the aviators' bodies," Mimika Transportation Agency air transportation division head John Rettob told reporters at the airport.
"The bodies will then be sent to the Indonesian Aviation Academy in Curug, Banten, on a plane chartered from Aviastar."
On April 9, Aviastar lost a BAE 146-300 jetliner that crashed in Wamena, Jayawijaya regency, killing all six crew on board.
Rettob, who is also the operator of Mimika Air, said the other bodies from Friday's crash were flown from Ilaga to Mulia, Sorong and Sentani.
"We coordinated with the Puncak Jaya regency administration to send three bodies to their families in Mulia," he said.
"We also contacted the families of Marthen Jitmau and Herman Senanfi in Sentani."
Marthen was the secretary of the Mulia General Elections Commission (KPUD), while Herman was the head of the Puncak Jaya Elections Supervisory Committee (Panwaslu).
Rettob said the evacuation was carried out by the Mimika Search and Rescue (SAR) team and PT Freeport Indonesia's Emergy Response and Rescue team.
SAR team chief Lt. Col. Easter Haryanto, who is also the Timika Air Force Base chief, lauded the SAR team and the Freeport team.
"We've handed the investigation over to the National Transportation Safety Committee *KNKT* to find out what caused the accident," he said.
The aviators' bodies were flown at 2 p.m. local time after being identified by the Papua Police's Disaster Victims Identification (DVI) team at the Mimika General Hospital morgue.
"We needed to identify the DNA of both victims, since the accident involved a foreigner," said DVI team chief Adj. Comr. Kiki Kurnia.
"The identification had to be done again because our team could not fly to Ilaga due to transportation difficulties."
The bodies were seen off by Mimika Police chief Adj. Sr. Comr. Godhelp C. Mansnembra, Mimika Transportation Agency head Markus Rautroma, Haryanto and Rettob, as well as other representatives of the Mimika regency administration.