A helicopter winched the body out of the rainforest and transported it to hospital, and the parents of missing 15-year-old Nora Quoirin later identified her.
She disappeared from the Dusun Resort, not far from Kuala Lumpur, on August 4, a day after checking in for a holiday with her London-based family.
Her family believed the teen, who had learning difficulties, had been abducted but police classified it as a missing person case.
More than 350 people were deployed to hunt through dense jungle, backed by helicopters, drones, sniffer dogs and divers, while traditional shamans conducted rituals in a bid to locate her.
The body was found in a small stream in a ravine about 2.5 kilometres from the resort, Malaysia's deputy national police chief Mazlan Mansor told a press conference.
Nora Quoirin. Source: The Lucie Blackman Trust/Family
He said the body was unclothed but declined to reveal if it had any injuries. Mazlan said it was still being treated as a missing person case.
"The family has confirmed it is the body of Nora," Mohamad Mat Yusop, police chief of Negeri Sembilan state, later told AFP.
A post-mortem will be conducted today, he said.
A group of volunteers who were part of the search and rescue team found the body after being tipped off by a member of the public.
A K9 Unit officer from the Royal Malaysian Police takes part in the search for 15-year-old Nora Quoirin. Source: EPA
As news emerged of the find, police vehicles raced to the area and cordoned it off while journalists descended on the scene.
The body was found in the official search zone, an area which the team had previously covered.
'Hearts breaking'
The grim discovery came a day after the family offered a 50,000 ringgit ($17,500) reward, donated by a Belfast business, for information that could lead to her return.
"Nora is our first child. She has been vulnerable since the day she was born," said a family statement.
"She is so precious to us and our hearts are breaking. We are appealing to anyone who has information about Nora to help us find her."
Family members gather at Tunku Jaafar Hospital (AAP) Source: AAP
At the weekend, her mother Meabh had fought back tears as she made an emotional speech thanking the search team, with the girl's French father Sebastien by her side.
The 12-acre (five-hectare) resort where the teenager disappeared from is next to a patch of thick jungle and in the foothills of a mountain range.
Her family had said it was extremely unlikely the reserved youngster would have wandered off on her own.
She has a condition known as "holoprosencephaly", which means she has a smaller-than-normal brain, has limited verbal communication and cannot write more than a few words.
She attended a school for young people with learning and communication difficulties.
While officially treating it as a missing person case, police had not ruled out other possibilities.
An open window was found in the cottage where the family was staying at the resort.
Police have questioned a number of people, examined fingerprints found on a window, and looked into reports that villagers heard a truck early on the morning that the girl disappeared.
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