The body was located on Thursday afternoon at Saibai and a formal identification process is underway.
Police have confirmed the body found at Saibai had injuries consistent with a crocodile attack.
They say investigations are ongoing into the cause of death.
It's believed a 16-year-old tried to swim to shore with a 13-year-old boy after their dinghy broke down overnight.
Police have said the 13-year-old boy raised the alarm when he reached land and is now safe with his family.
It's believed the rain and wet weather prevented the teenager from reaching the shore.
ABC reported that Queensland Police Torres Strait Acting Inspector Anthony Moynihan wasn't certain the boat had been located, believing it broke down 500 metres north of Saibai.
However, the Department of Environment and Science says it was made aware of the incident.
