"All of the children have safely been removed from the ranch," Child Protective Services spokeswoman Marleigh Meisner told reporters in nearby San Angelo.
But Meisner said the agency still didn't know whether the 16-year-old was among the children pulled from the compound on the grounds that they were all in danger of "emotional, physical, and-or sexual abuse."
The documents said that investigators discovered a number of teen girls who appeared to be pregnant as they searched the compound.
"Investigators determined that there is a widespread pattern and practice of the (Yearn for Zion) Ranch in which young, minor female residents are conditioned to expect and accept sexual activity with adult men at the ranch upon being spiritually married to them," read the affidavit signed by Lynn McFadden, a Department of Family and Protective Services investigative supervisor.
McFadden said that as soon as girls reached puberty, they were spiritually married to an adult male and required to produce children.
The Texas investigation is the state's first with FLDS, but prosecutors in Utah and Arizona have pursued several church members in recent years, including sect founder Warren Jeffs, who is serving two consecutive sentences of five years to life for being an accomplice to the rape of a 14-year-old wed to her cousin in Utah. He awaits trial on other charges in Arizona.
An unknown number of men were being held at the ranch while authorities completed the search of the gleaming 80-foot-high temple, a cheese-making plant, a cement plant, a school, a doctor's office and housing units.
Authorities have described FLDS members as cooperative, but the house-by-house search of the temple, factories and living quarters has triggered some trouble.
On Monday, 41-year-old Leroy Johnson Steed was arrested on charges of felony tampering with evidence -- a day after 19-year-old Levi Barlow Jeffs was arrested on misdemeanor charges of interfering with the duties of a public servant, said Department of Public Safety spokesman Tom Vinger.
He declined to give details on the arrests or if Levi Barlow Jeffs might be related to FLDS leader Warren Jeffs.