During today's hearing, however, the state argued that the children not be returned to the sect's ranch in Eldorado, Texas.
Gary Banks, a lawyer representing Child Protective Services, told the judge the state believes "there is a systematic process at the ranch near Eldorado at which children were exploited and sexually abused."
Authorities raided the compound April 3 after a domestic violence hotline recorded a complaint from a 16-year-old girl who said she was physically and sexually abused by her 50-year-old husband.
If the state retains custody, the children could be placed in foster homes, at least temporarily — another massive undertaking for children raised in the insolated religious sect.
"I think they find themselves suddenly in a very strange world," the Rev. Michael Pfeifer, Bishop of San Angelo, who has toured the shelter, told ABC News.
Pfeifer and others who have been inside the temporary shelters told ABC News that the women and children repeatedly said they wanted to go home. Pfeifer said the conditions inside the shelter were cramped, with cots lined up close together and lots of women tending to infants.
At least one mother, who said she was separated from her older daughter, appeared angry, according to Dr. Stephen Smith, who has treated some of the families. The tearful woman said that state authorities had moved her teenage daughter because they wanted to speak to the girl further.
Smith said he is upset by what he has seen there.
"All of the mothers and children that I spoke with wanted to go back to the ranch, without a doubt," Smith told ABC News. "Personally, it makes me very sad for what we have done." When asked if they were afraid, the women replied, 'Of course not, we have unwavering faith,'" Smith said.
Smith added that the women also said they would forgive state authorities for what they had done.
Some mothers from the Eldorado sect toured the compound's empty homes with reporters and photographers from the Deseret News, a Utah newspaper owned by the Mormon church.
"We are not child abusers. The only abuse they've ever had is since the CPS [Child Protective Services] has taken them," a mother named Shannon told the newspaper.
The mothers say the conditions at the state shelter are so cramped that the children are scared and many are sick. At least a dozen children have contracted chicken pox.
Smith said he talked to a little boy about 7 or 8 who said he liked to sing, and then broke into the hymn, "Mighty Fortress of God."
Texas officials say the state was absolutely right to take custody of all the children.
"These children are with us because we believe they have been abused or neglected, and at this point in time, no one else is going to be visiting those children," said Marlay Mesiner of the Texas Family and Protective Services.
Over the weekend, the court authorized a request by officials to confiscate cell phones from sect mothers who were with the children in the shelter. The state's request said it was necessary to prevent "intimidation and tampering with child witnesses."
The teen who made the call for help that prompted the raid has yet to be identified.
The man whom the teen named as her husband, Dale Barlow, a convicted sex offender, was interviewed by Texas Rangers over the weekend in Utah.