Wayne Bent left the city-county lockup in the small northeastern New Mexico town of Clayton about 3 p.m., Police Chief Scott Julian said.
"He is no longer in our custody," Julian said.
Bent was released after his son, Jeff Bent, gave the Union County Magistrate Court in Clayton a cashier's check for $55,000, according to Michelle Jones, chief clerk of the court.
Conditions of Bent's release include not leaving the county without court permission and having no contact with the alleged victims or other minors unless they're blood relatives.
Wayne Bent, 66, who heads The Lord Our Righteousness Church and calls himself Michael Travesser, was charged on Tuesday with three counts of criminal sexual contact of a minor and three counts of contributing to the delinquency of a minor.
The charges are felonies.
His bond was initially set at $500,000, but was lowered to $55,000 during his first court appearance on Thursday, in magistrate court.
District Attorney Donald Gallegos said he will convene a grand jury within the next two weeks and seek indictments against Bent.
Bent and his followers have lived on a former ranch in a remote part of the county near the New Mexico-Colorado line since 2000. Bent has said he is the Messiah and acknowledges having lain naked with virgins. Jeff Bent said his father has committed no crimes.
Wayne Bent had refused to eat or drink at the jail for a couple of days, but drank orange juice after his Thursday court appearance.
Julian said Bent's followers brought him juice and food later Thursday and Friday, which he ate. Members of the sect are vegetarians.
"He wasn't a problem prisoner at all," the chief said.
The state Children, Youth and Families Department recently removed three teenagers, two girls and a boy, from the sect's compound, which they call Strong City. The district attorney says he doesn't believe any minors are living there currently.