A Family Court ruling by Judge Paul Geoghegan ordered the children's main carer should be their father, and the judge placed constraints on the children's participation in the Jehovah's Witness faith.
Both parents appealed against the ruling and sought clear directions regarding the children's participation in the faith.
The mother told the court she would not attend a concert one of her children was involved in, because it was being held at a Baptist Church.
She also did not attend her other child's soccer prizegiving, because it was also held at the church.
The children told Justice Brown that if they were not allowed to worship Jehovah by attending services, they would be "angry" and "sad".
He said the children had a right to be exposed to each of their parents' religious beliefs and it would be "impractical" to prevent their involvement in their mother's faith.
"Indeed it would be my view it would be counter-productive and possibly destructive to order otherwise."
However, he felt that involvement should be curtailed.
"...the children should not attend Jehovah's Witness meetings or church activities including seminars or witnessing.
"I recognise that such a direction is at odds with the children's express wishes.
"Nevertheless the evidence persuades me that their welfare and best interests require that there should be a dilution in the intensity of their exposure to their mother's faith."
They could engage in Bible study, watch videos and read passages from the Watchtower while they were with their mother in her home, Justice Brown said.
They could also attend birthday parties, and Easter and Christmas celebrations -- all of which are prohibited in the Jehovah's Witness faith.
