The boy’s family reported his absence to police after searching for several hours on Friday.
Northern Territory Police mounted a search and rescue operation on Friday night and found the child, aged under five, early on Saturday morning.
He subsequently passed away.
On Sunday afternoon, acting Assistant Commissioner Sachin Sharma said officers were interviewing witnesses to determine the circumstances behind the disappearance and death.
Police offered their sincere condolences to the family and have requested that the family’s privacy is respected at this time.
A report will be prepared for the coroner.