Sahib Ali, hailing from Assam's Chirang district, is one of the five men who narrowly escaped the flooding coal mine a fortnight ago.
However, the National Disaster Response Force, which has been engaged in the rescue operation since the day of the tragedy on December 13 last, will continue with their services.
The officials said the body was spotted at a depth of more than 200 feet inside the "rat-hole" mine and naval divers brought it to its mouth.
On skeletons being seen by the Navy team, the sources said the water inside the mines has high Sulphur content which can decompose the bodies very fast.
The Navy wanted to ascertain the water level as their divers can operate up to 100 feet in a closed container-type situation, a district official said.
The body has been detected inside the 370-foot-deep coal mine in Meghalaya's East Jaintia Hills district,
The depth of water from the surface till the bottom of the pit is expected to be over 150 feet, Navy officials said.
Rigorous pumping of water from the nearby abandoned mines is expected to begin on Friday.
The miners are now feared dead as water from a nearby river has been gushing into the 370-feet-deep pit.
Two teams of the National Disaster Response Force consisting of over 60 personnel reached on Friday morning, while 12 personnel from the State Disaster Response Force are already at the site.
The body, located 200 feet away from the bottom of the mine, was brought out using the Indian Navy's underwater remotely operated vehicle and an National Disaster Response Force boat on Wednesday, said operations spokesman R Susngi.
At least 15 miners were trapped in the 370 foot-deep illegal coal mine in Lumthari village of East Jaintia Hills district since December 13 and all efforts to pump the water out of flooded mine have been in vain.
The 15-member team, equipped with specialised diving equipment including a re-compression chamber and remotely operated vehicles capable of searching underwater, went straightway to the mine site in the remote Lumthari village in East Jaintia Hills district.
Pump manufacturing company Kirloskar Brothers Ltd and Coal India on Friday are jointly moving 18 high-powered pumps to the mine, officials said.