He revealed that a psychiatrist involved suggested the children's mother had not only allowed but even encouraged the "demonisation" of her former partner.
The judge said that, while he can't give more specific details, he felt the public needed to be aware of the case and how these situations can happen.
The magistrate called it an example of "how badly wrong things can go" when one parent alienates the other.
He said the man "plainly" loved his children and spent eight years fighting for them.
"No professional has suggested that there is anything about this father that renders him unsuited to have contact with his children," the judge wrote.
"There have been consistent recommendations throughout the eight-year history of these proceedings from a wide spectrum of professionals that contact should take place between the father and the children.
"All professionals involved in this case have concluded that the mother has alienated the children from the father," he added.
The children reportedly wanted nothing to do with their father or his side of the family. They refused to acknowledge cards or presents and had "false memories" of their interactions with their dad.
"I am afraid that the cause of that harm lies squarely with this mother," Judge Wildblood wrote.
"Whatever may be her difficulties, she is an adult and a parent with parental responsibility for her children.
"That parental responsibility, which she shares with the father, requires her to act in the best interests of her children," he said.
"It also required her to promote the relationship between these children and their father. She has failed to do so."
In his ruling, he expressed how sorry he was for the father. "This has been a long, heart-breaking and expensive set of events for you to endure. I am truly sorry," the judge wrote.
