In written and oral testimony provided to lawmakers Wednesday, officials with the state Department of Family and Protective Services said interviews and journal entries suggested that boys may have been sexually abused.
Earlier, the department's commissioner, Carey Cockerell, told lawmakers that at least 41 children, some of them "very young," have evidence of broken bones.
The state has custody of 464 children from the Yearning For Zion Ranch in the west Texas prairie town of Eldorado, including a baby born to a teen mother Tuesday.
Although Cockerell didn't elaborate on the broken bones, a report by his department's Child Protective Services division said medical exams and interviews indicated "that at least 41 children have had broken bones in the past."
"We do not have X-rays or complete medical information on many children so it is too early to draw any conclusions based on this information, but it is cause for concern and something we'll continue to examine," the CPS report said.
The state Senate Health and Human Services Committee's hearing on Texas' foster care system had been planned for Wednesday before the April 3 raid on the ranch. But for the morning part of the hearing, the polygamous sect took center stage.
The state has been criticized for taking all the children from the ranch, including infants and boys, on the theory that the girls may be abused when they are teens.
State authorities raided the ranch in search of evidence of underage girls being forced into polygamous marriages. Since then, the state won temporary custody of the children, now scattered around the state in group foster-care facilities.
FLDS spokesman Rod Parker called Cockerell's testimony "a deliberate effort to mislead the public."
Although the ranch has a small medical facility, Parker said any broken bones would have been treated away from the ranch and that doctors are required to report suspected abuse.
Parker said state officials were "trying to politically inoculate themselves from the consequences of this horrible tragedy."
Cockerell told a legislative committee the investigation has been difficult because members of the church have refused to cooperate.
Mothers who stayed with their children for two weeks after the raid launched a coordinated effort to stymie investigators, coaching their children to not answer questions, Cockerell said.
He said the women and children would gather into apparent family units, with the children referring to several women as their mother, then the "women switched children in these family units ... making it difficult."
"When asked, women and children would change their names and ages," he said.
The CPS report also said authorities "tried to use bracelets to identify children, but the women and children removed the bracelets or rubbed the wording off them."
The report also said mothers at first refused to let the children undergo basic health screenings and that "many" teen girls declined to take pregnancy tests.
On Monday, CPS announced that almost 60 percent of the underage girls living on the Eldorado ranch are pregnant or already have children.
Under Texas law, children under the age of 17 generally cannot consent to sex with an adult. A girl can get married with parental permission at 16, but none of the sect's girls is believed to have had a legal marriage under state law.
Church officials have denied that any children were abused at the ranch and say the state's actions are a form of religious persecution. They also dispute the count of teen mothers, saying at least some are likely adults.