Four other personnel, who were injured in the attack, have also been brought back in a UN chartered aircraft.
The five army personnel killed in the incident were Lt Col Mahipal Singh, Naib Subedar Shiv Kumar Pal, Havaldar Hira Lal, Havaldar Bharat Singh and Sepoy Nand Kishore. They belonged to the 6 Mahar regiment and the 9 Mechanised Infantry battalion.
The body of Lt Col Singh, who belongs to Mahendragarh in Haryana, was taken to his native place in an ambulance by road. The IAF's AN-32 and Avro aircraft would be used to send the bodies to far off places such as Pithorgarh in Uttarakhand and Midnapore in West Bengal.
UN secretary general Ban Ki-Moon has condemned the attack saying it could amount to a war crime. The South Sudan Government has blamed followers of rebel leader David Yau Yau for the ambush.
Government forces have been battling the rebels in Jonglei while UN peacekeepers are trying to maintain order and minimise civilian causalities.