Negri Sembilan police chief Datuk Mohamad Mat Yosuf announced that the 15-year-old's parents, Sebastian Quoirin and Mebah Quoirin, identified the body that was found in a jungle area near the Dusun resort was their daughter.
Her body was found in the Betembum mountains by members of the Seremban hikers club, who had joined police, residents and members of the indigenous Orang Asli people in the search and rescue operation.
The Lucie Blackman Trust (LBT), which has been providing assistance to the Quoirins, said in a statement that it could "confirm with great sadness that the body found today is that of missing teenager Nora Quoirin".
He tweeted: "Our thoughts & honest condolences are with Nora Quoirin's parents, siblings & wider family at this unimaginably hard time".
"It was found two kilometres (1.2 miles) from the Dusun Resort where she was staying".
Her father raised the alarm at 08:00 local time the next day after she was discovered missing from her bedroom.
Authorities had begun a criminal investigation into the disappearance, he said, although an initial investigation revealed no evidence of criminal behaviour.
Police believe the teen, who has learning and physical disabilities, climbed out through an open window in the living room of the resort cottage.
Her parents offered a £10,000 ($12,000) reward for information leading to the return of their daughter, after receiving a donation from an anonymous business in Belfast, Northern Ireland. The girl's family says she isn't independent and wouldn't wander off alone, and was likely to have been abducted. "She is so precious to us and our hearts are breaking", her parents Meabh and Sebastien Quoirin said on Monday, as the search entered its ninth day.
Appearing before cameras on Monday, a tearful Ms Quoirin said: "Nora is our first child. To all our friends and family at home, we can't thank you enough for all your love".
The body "was not in any clothing" and was found by volunteers, national deputy police chief Mazlan Mansor said according to the New York Post.
The Irish News reports that a special Mass was being held in Nora's honour at St. Brigid's Church in south Belfast on Tuesday.
"She has truly touched the whole world".
She added: "We had heard that she was excited about seeing the waterfall when she arrived at the resort".
The Lucie Blackman Trust, which was set up in the wake of the murder of a British hostess in Japan in 2000, said: "At this time we can not confirm it is Nora".
Malaysian sharmans and police from Britain, Irish and French were among those drafted in to assist.