His body was retrieved on Thursday morning by defence personnel along with bodies of four others who were killed on April 30 chopper crash at Keyla heights near Luguthang in Tawang.
The body in a coffin wrapped in a tricolour was carried from the helipad to the official residence of the chief minister in a flower bedecked vehicle to facilitate paying last rites by the people.
Arunachal government has declared seven days of state mourning in respect of its departed chief minister.
The post-mortem was conducted at the army post at Tawang. However, last rites of Khandu will be performed at his native village at Tawang after the body is taken back there from Itanagar.
Thousands of grief-stricken people, some of whom have come from far flung areas, were seen waiting eagerly at the Itanagar helipad to pay their last respect to their beloved chief minister.
All the senior political leaders of Arunachal Pradesh, Congress ministers, representative of governments of other states in the North East were also waiting at Itanagar helipad for the body to arrive.
Earlier in the day, the army, with the help of locals, brought the bodies of Arunachal Pradesh Chief Minister Dorjee Khandu and four others from Keyla, where the helicopter with five on board crashed on Saturday last.
Keyla is located at an altitude of 4,500 meters and about six-hour trek on foot away from Luguthang Gompa in Tawang district.