State Police Director Col. James Baker said Brooke Bennett's body was found about 4:45 p.m. and her family had been notified.
The uncle, Michael Jacques, has been in custody since Sunday on charges of aggravated sexual assault against a different underage girl. He has pleaded not guilty.
Brooke was last seen alive with Jacques at a convenience store a week ago.
"The painful discovery of Brooke's body today is tragic and heartbreaking," Baker said at a news conference.
He called the death "clearly suspicious" but declined to give details before a planned briefing Thursday morning.
But in an affidavit unsealed earlier in U.S. District Court in Burlington, the FBI said an unidentified teenager told investigators she was present on June 25 when Jacques, 42, tricked Brooke into thinking she was going to a party and took her to his Randolph home to be initiated into a sex ring.
The girl said she was led to believe that Brooke would "would have sex with adult males" during the initiation.
After the three got to Jacques' home, the girl said she and Brooke watched television for a while before Jacques told her to leave and took his niece upstairs. The witness, who is 14, said she left the house with her boyfriend and did not see Brooke again.
The 14-year-old said she herself had been having sex with Jacques since she was 9 as part of the sex ring.
Brooke's former stepfather, Raymond Gagnon, appeared in federal court Wednesday on an obstruction of justice charge in the case. He was denied bail and was held pending another hearing on Monday.
Police say Gagnon, 40, lives in Texas but often visited Vermont. According to the affidavit, he told police he accessed Brooke's MySpace page from a laptop computer at his home in San Antonio after getting login information from Jacques.
Police said they have evidence that postings to the account were altered to make it appear that Brooke had discussed a secret rendevous with someone identified as "Skittlemeup" shortly before she disappeared.
Gagnon also told police he had downloaded child pornography onto the laptop, according to the affidavit.
In Randolph before the announcement, Brooke's friends and family put up signs saying they missed her and were praying for her safe return. She lived in Braintree, a small town close to Randolph.
"To the community, thank you so much for all your support and help, and I hope I can keep continuing to get that," said Brooke's mother, Cassandra Gagnon. She wore a photo pin of her daughter on her T-shirt.
She said she was "very surprised" by her ex-husband's alleged involvement.
Mom Accused of Denying Son Chemo
A woman has been charged with withholding cancer medication from her 8-year-old autistic son, who prosecutors say likely will die because the cancer has returned.
Kristen Anne LaBrie, 36, of Beverly, was released on personal recognizance Monday after pleading not guilty in Salem District Court to a charge of reckless child endangerment.
Her son, Jeremy Fraser, had been in remission from non-Hodgkin's lymphoma.
He had a good prognosis when first diagnosed, with chances of recovery put at 85 percent to 90 percent, according to a police report. But his chances have dropped to 10 percent since being deprived of medication, authorities said.
Prosecutor Kate MacDougall said "in all likelihood, Jeremy Fraser will not see his ninth birthday."
"This child was in remission," she said. "His prognosis was good. This child came out of remission. ... He is not expected to survive."
Labrie declined comment to the Salem Evening News as she left court. Her lawyer, Kevin James, said Labrie had taken her son more than 100 times to Massachusetts General Hospital and "has been extensively involved in this child's care."
He said prosecutors had "a very weak case."
According to a police report, Fraser was diagnosed with non-Hodgkin's lymphoma in 2006 and underwent a five-phase regimen of chemotherapy, including drugs that were supposed to be given to him at his house by his mother.
Police said LaBrie canceled at least a dozen appointments for chemotherapy treatments. MacDougall also said LaBrie did not fill at least half of the prescriptions her son was given.
In March, Dr. Alison Friedmann, the child's oncologist at Massachusetts General Hospital, filed a report of suspected neglect with the Department of Social Services after discovering Fraser's cancer had returned, something that should not have happened if he was on his medications.
The boy's father, Eric Fraser, now has full custody of his son in Saugus. He said Jeremy spends part of his day in a special education program.
"The kid's a peach," he said. "He doesn't do one bad thing."
Eric Fraser said he's outraged LaBrie did not have to have to post bail Monday.
"I'm pretty disgusted about the whole justice (system) and DSS," Fraser said. "Now my son's going to die."