The fuselage will now be taken to Karwar for inspection.
The Navy had already recovered the Black Box, which will now be inspected as a part of the Board of Inquiry.
The fuselage was brought up with the help of a Naval ship, the Defence sources said.
The Indian Navy surveillance aircraft had crashed south-west off Goa coast on Tuesday with the three officers on board. Commander Nikhil Kuldip Joshi, who was flying the aircraft and has 4,000 flying hours to his credit, was rescued about an hour after the crash by a fishing vessel.
The navy had launched an extensive search and rescue operation to find the two missing officers.
At least 12 ships, including two of Indian Coast Guard, and four aircraft were involved in the rescue operation.
