The body found was that of a four-year-old boy, I Putu Sudayana, head of the Maumere, Flores Island, search and rescue office, remarked here on Sunday.
The child's body was found on Margeta Beach, not far from the location where the ill-fated boat sank on Saturday at 3 a.m. local time.
With this latest finding, the death toll has reached three, while four passengers are yet unaccounted for.
"We will continue to look for the missing passengers of MV Nusa Kenari 2," he stated.
The search and rescue team constituted local disaster mitigation and SAR officers, police and military personnel, as well as volunteers.
The Alor Police in East Nusa Tenggara Province had earlier reported that two passengers died and five others went missing after MV Nusa Kenari 02 sank.
The ill-fated boat's skipper, Piterson Plaituka, 30, and three crew members survived and were currently undergoing police interrogation, Adjunct Senior Commissioner Patar Silalahi, the Alor Police chief, remarked here on early Sunday.
"We are still questioning the four crew members to unearth the cause behind the sinking of MV Nusa Kendari 02 on Saturday," Silalahi noted.
MV Nusa Kenari 02, with tens of passengers onboard, sank in the waters of Tanjung Margeta, Alor District, en route to Mademang Village, Pureman Sub-district, in East Alor, from Kalabahi, the capital of Alor District, on early Saturday.
The boat had cargo and 52 people onboard. Following the accident, 45 people were rescued, four were slightly injured, two died, while five others comprising two adults and three children remain missing.