The rescue team discovered the body just after dawn on Monday, floating near the northern waters of Serai island, about 1km from the site of the sinking, after a local resident spotted the victim, said Fathur Rahman, the Maumere Search and Rescue Office chief.
He said the body was transported to a hospital in Labuan Bajo, a gateway town to eastern Indonesia's Komodo National Park, for identification.
"Relatives of the victim joined the ambulance to ensure identification through medical and forensic procedures," Rahman said.
The family holiday in the park area turned tragic for Valencia CF Women's B coach Fernando Martin, 44, when the boat also carrying his wife, their four children, four crew members and a local guide, went down on Friday evening after suffering engine failure on a trip within the park that attracts thousands of international visitors for diving, trekking and wildlife tours.
Martin's wife and another child, along with four crew members and a local guide, were rescued in the hours following the incident.
But Martin, his two sons and another daughter, aged nine, 10 and 12, were unaccounted for.
Rahman said Martin's wife, Andrea, their youngest daughter, Mar, and other survivors were in good health and that authorities are investigating the cause of the accident.
Komodo National Park is a UNESCO World Heritage site famous for its rugged landscapes, pristine beaches and the endangered Komodo dragon.
The search operation, on its fourth day Monday, continues for the remaining family members.
The search area had been doubled from the initial one centred on a 9km radius from the site of the sinking, where rescue teams found the boat debris, Rahman said.
In a statement on X, the Valencia CF football club expressed condolences, calling the tragedy "a devastating loss" for the club and its community.
Spain's La Liga expressed its heartfelt support in a message of solidarity while other football clubs, including Real Madrid and Barcelona, also offered condolences.
Indonesia is an archipelago with more than 17,000 islands, where boats are a common form of transportation.
With lax safety standards and problems with overcrowding, accidents occur frequently.
