A North Carolina judge presiding over a bitter divorce case has ruled that three home-schooled children must start attending public school — a decision their mother angrily says was based on her religious beliefs.

Wake County Judge Ned Mangum granted Thomas and Venessa Mills joint custody of their children — ages 10, 11 and 12 — and ruled that the children's "best interest" would be served by sending them to public school this fall, according to a temporary custody order.

But Venessa Mills insists her association with the Sound Doctrine Church played a "big factor" in Mangum's ruling, in which he also ordered her to undergo a mental health assessment within 30 days.

"He disregarded the facts and said that even though the children are thriving in home school, they'd do better in public school," Venessa Mills told FOXNews.com. "It's a clear cover-up by the judge. He made a bad ruling about home schooling and he is clearly covering his tracks."

Venessa Mills, whose home-school curriculum includes swimming, piano lessons and instruction from Sound Doctrine members via phone and Web cam, claims Mangum showed his bias by not including rebuttals to damaging testimony by her relatives and close friends in his ruling.

"He said that public school will challenge the ideas that I taught them," Mills said. "My children have clearly stated they do not want to go to public school. They want to remain at home school ... so why rip them out?"

Mangum disputed that claim in his order released Tuesday, ruling that the children's father, Thomas Mills, has the right to expose his children to alternative views.

"As previously stated in open court, while this Court clearly recognizes the benefits of home school, and any effort to characterize it differently is incorrect, it is Mr. Mills' request to re-enroll these children back into the public school system and expose them and challenge them to more than just Venessa Mills' viewpoint," Mangum wrote.

"Contrary to Ms. Mills' requested relief, this Court can not and will not infringe upon either party's right to practice their own religion and expose their children to the same."

According to court documents, the Millses had a "strong and happy" marriage until 2005, when Venessa Mills joined the Sound Doctrine Church in Enumclaw, Wash.

At that point, her husband testified, she "became unrecognizable as the person" he had married.

"She withdrew emotionally from me," said Mills, who admitted to having an affair.

Venessa Mills' mother, Dawn Lewis, told the judge she soon became "concerned" about her daughter's involvement with the church and its effect on her grandchildren.

The church was described by as a "cult" by former members, according to court documents.

"Sound Doctrine is not a healthy place for kids to grow up," former member Tina Wasik testified. "It is run by fear and manipulation."

Referring to the church's leaders, Tim and Carla Williams, Wasik said, "Timothy and Carla manage to ruin relationships between man and wife and parents and kids."

Jessica Gambill, another former church member and acquaintance of Venessa Mills, testified that Tim Williams made several inappropriate sexual comments about girls as young as 4 years old.

"After I joined Sound Doctrine, Tim Williams told me that my oldest daughter (then age 12) was the kind of girl men would take advantage of, that my middle daughter (then age 7) was the kind of girl that would sleep with any guy, and that my youngest daughter (age 4) was the kind of girl that would use her looks to seduce men," Gambill testified.

The accusations against Sound Doctrine were denied by church officials and in affidavits filed by Venessa Mills' attorney.

"They're completely false," Malcolm Fraser, an assistant pastor for Sound Doctrine, said of the accusations. "Clearly someone has an ax to grind with the church."

Attempts to reach Thomas Mills were unsuccessful. Calls to his attorney, Jaye Meyer, were not returned.

The judge indicated that his ruling had nothing to do with Venessa Mills' religious beliefs — and rather that her husband should be allowed to "expose their children to more than just the experiences that [she] desires" — supporters say Venessa Mills was wronged.

Robyn Williams, a home-school mother who has chronicled the divorce proceedings at hsinjustice.com, accused Mangum of attacking both Venessa Mills' character and her church.

"He is diverting attention from his own biased decision and is attacking the church because he knows he's wrong," Williams told FOXNews.com.

"If the roles were reversed, do you really think the judge would have ordered them to be subjected to home schooling?"