The missing girl prompted a wide-ranging search by hundreds of volunteers over the long holiday weekend.
Richard Adams, 24, was charged with murdering his daughter, Kayla McKean, in a fit of rage and then burying her in a remote area of central Florida.
Kayla's stepmother, Marcie Adams, led investigators to Kayla's shallow grave Monday.
Adams said he hit the girl repeatedly and threw her against a wall, according to an arrest affidavit. At one point during his confession, Adams told police he may have used a wooden "discipline" paddle on his daughter.
Capt. Chris Daniels, a spokesman for the Lake County Sheriff's Office, said Ms. Adams is cooperating with investigators, who offered no motive for the killing.
Earlier Monday, Kayla's mother said she was given a polygraph test.
"They're doing their best to find Kayla, and I'm confident they will find her," Elizabeth McKean said. "They have to narrow it down to everybody, so I'm not taking offense [at being questioned]."
Police said Kayla was at school on Tuesday but did not go to school on Wednesday.
The body was found near a creek southeast of the popular Alexander Springs Recreation Area in the Ocala National Forest, a favorite spot of Kayla's, according to family friends.
Hundreds of volunteers began searching for Kayla on Thanksgiving Day when her father reported her missing to authorities.
CBS News Correspondent Dawn Stensland reports that the volunteer searchers broke into tears and prayers when they were told the girl was dead.
Their prayers for Kayla became a curse for her father.
"They should let us do to him what he did to the child," said one searcher.
Kayla had lived with her mother in the Orlando suburb of Casselberry for her entire life until last April, when she moved in with her father and stepmother.
The search for Kayla continued through the weekend, and pictures of the girl were mailed out Monday to 2,000 Texaco gas stations around the country.
Ms. McKean refused to talk to reporters as she left a police command center Monday night, clutching a teddy bear a girl had given her several days before.
"The support of the community is what kept her going throughout all this," said Don Wood, president of Child Watch, a child advocacy group that has been helping Ms. McKean.
Sheriff's officials have said state social workers had investigated Kayla's father on at least three occasions. Court records show Adams has a history of violent behavior dating back to 1992 and has served jail time for assault and other crimes.