A father who was given good behaviour bonds for repeatedly raping his young daughter will go to jail for at least three years after an appeals court found the original sentences "were erroneously lenient and manifestly inadequate".

A series of mistakes led to the man avoiding a prison sentence for sexually and indecently assaulting his daughter when she was aged between nine and 12, including occasions when her mother was at a Sunday morning church service.

"Very disturbed by the sentence:" NSW Attorney-General Greg Smith. Credit:Rob Homer

Instead, he was referred to a two-year residential treatment program known as Cedar Cottage in Westmead, which was designed for men who had pleaded guilty to incest.

The Attorney-General, Greg Smith, bought the appeal after the Director of Public Prosecutions declined to act. He also axed the Cedar Cottage program.