Judge Barbara Walther, who ordered the children kept in temporary state custody, said that siblings should be kept together, that babies younger than one year old should stay with their mothers and that breast-feeding mothers with children between the ages of one and two should be allowed to live near their toddlers.
But the logistics of placing more than 400 children into foster homes are proving to be a nightmare.
Mary Golder, an attorney for five sisters from the Fundamentalist Church of Jesus Christ of Latter Day Saints, said one was left behind.
"It would be devastating for this 4-year-old to be separated from her sisters and sent to live in Houston with strangers," she said.
State officials admit this will be difficult but insist it is necessary.
"No matter how badly a child is abused they always want to be with their parent. Unfortunately that is not always in their best interest," said Darrell Azar, a Child Protective Services spokesman.
The children were taken into state custody by Texas authorities, who raided the FLDS ranch after they said a person claiming to be a 16-year-old girl called a hotline to report that she was being abused by her 49-year-old husband.
The children are being housed until they have individual status hearings. Some children could be placed in permanent foster care. Some parents who have left the sect may win custody, while some kids may be allowed to return to the ranch in Eldorado.
In a related development, court documents unsealed Wednesday revealed that a phone number used to allege abuse at the ranch is associated with a woman in Colorado who has been accused of making several unrelated false abuse claims in calls to authorities.
An arrest warrant affidavit said 33-year-old Rozita Swinton had previously used a phone number to call the crisis hotline in Texas that received the calls prompting the raid.
The calls came before authorities raided the Yearning for Zion Ranch on April 3, but it was not clear whether authorities believe Swinton made the calls that triggered the raid.
Swinton has not been arrested for allegedly making calls to the Texas shelter. She was arrested last week on charges of making a false report in an unrelated case.
The affidavit details dozens of calls from late 2006 through April 2008 to abuse centers and police departments in Washington, Colorado and Texas. The callers always identified themselves as a young girl, at various times calling herself Dana, April, V, Jennifer and Sarah Barlow. Sarah Barlow is the name of the 16-year-old who called the Texas crisis center.
The Colorado court documents say that a phone number associated with Swinton, who has been named by Texas Rangers as a "person of interest" in their investigation, was "possibly related to the reporting party for the YFZ ranch incident."
The affidavit says that in one call to a safe house in Colorado a person calling herself Dana said she had been sexually abused. Dana told the safe house counselor in February 2008 that she and Rozita were different personalities who lived in the same body, according to the affidavit.
Dana then told the counselor to call back on Rozita's number and gave Swinton's home phone number, the affidavit says.
Another number that was used to call the Texas abuse hot line has been linked to a man named Courtney Swinton, who lives in the same apartment building with Rozita Swinton, according to the affidavit.