The body of Major Amit Deshwal, killed in an encounter on Thursday, was on Friday recovered from a remote place in Tamenglong district and flown to Jorhat from Imphal.
The body will then be taken to Surheti in Jhajjar district of Haryana via New Delhi for the last rites.
Major Deshwal, who belonged to 21 Para SF, was paid tributes with full military honours. His father, Subedar (Retd) Rishi Deshwal, was the first to lay the wreath on the coffin, a Defence spokesperson told PTI.
Manipur governor V Shamunagathan, chief minister O Ibobi Singh, deputy chief minister Gaikhangam and other senior army officers, including the GOC of Nagaland-based III Corps, paid tributes and laid wreaths on the coffin.
Major Deswal was killed in a gunbattle with ZUF militants in densely forested Nungba area during a combing operation undertaken by Rashtriya Rifles and Special Forces personnel.
The post-mortem on his body was conducted at Regional Institute of Medical Sciences, army officials said.
He is survived by his wife and a three-and-half-year old son.
One militant was also killed during the gunfight.
For the time being, the combing operation which was going on for the last few days has been called off by the Army, the officials added.