Malaysia's deputy inspector general of police, Datuk Mazlan Mansor, said there was "reasonable suspicion" that the body of the "Caucasian female" found 1.2 miles from the Dusun resort was that of Nora, who is of Irish and French descent.
Her body was found just over 2km away from the Dusun, according to BBC correspondent Howard Johnson.
A postmortem examination was expected to be carried out on Wednesday to determine the cause of death and whether police will carry out any further investigations.
Nor did they find any footprints inside the villa or forensic evidence to suggest an unknown person was inside.
National deputy police chief Mazlan Mansor said the body was found beside a small stream about 2.5 kilometers (1.6 miles) from the Dusun eco-resort in southern Negeri Sembilan state where Nora Anne Quoirin went missing on August 4.
"The search and rescue team will still be on standby. our team is still at the scene where the body was found", he said.More news: Jeffrey Epstein guards suspected of falsifying logs at Metropolitan Correctional Center
The incident drew worldwide attention and support for the family, including from Garry Kasparov, a Russian former world chess champion.
Tuesday's discovery came the day after Nora's mother, Meabh Quoirin, made an emotional appeal for help - and an anonymous Belfast-based business offered a reward of nearly $12,000.
President of Ireland, Michael D Higgins, said: "Sabina and I offer our deepest condolences to Nora's parents, Meabh and Sebastien, to Nora's siblings and to her extended family".
He tweeted: "Irish + French embassies in Malaysia working together to provide every assistance to the Quoirin family".
Police believe the teen, who has learning and physical disabilities, climbed out through an open window in the living room of the resort cottage. "Please be patient. We will let you know as soon as it's confirmed", an officer told The Mirror.More news: Chandrayaan-2 leaves earth's orbit, moving towards moon: ISRO
Giving more details of her special needs last week, her parents explained that she read like a young child, could not write more than a few words, and was unable to do maths, making money impossible to manage.
The Quoirins had said Nora's condition meant she was not independent and had difficulty walking. She has been vulnerable since the day she was born, ' she said.
Police are not ruling out criminal elements in the case, have questioned witnesses and are investigating witness accounts of a truck heard early on the morning the girl disappeared.
Malaysian sharmans and police from Britain, Irish and French were among those drafted in to assist.
Nora's parents, who have lived in London for 20 years, had previously expressed fears that the schoolgirl had been abducted and had put up a £10,000 reward for information.More news: Flint Bishop Airport adding new nonstop flights to Florida