"Parents have ample opportunity to teach children about the Bible outside school time," Mr Harnett said yesterday.
The Browns Bay Presbyterian Church wrote to the board in May opposing the decision.
As well, some parents felt they had not been consulted. "The [most frustrating thing] was that no one told us, it just happened," said one, Marianette Moller.
She said the classes benefited her son Daniel, 9, because they taught Christian values as well as the Bible.
Campbells Bay School's religious programme was shut down this year because of a lack of parental support.
Robin Palmer, of Browns Bay Presbyterian Church, was concerned that children whose schools did not use the Bible in Schools programme would be at a disadvantage. "We regard the programme as adding value to the school, and it's been around for many years."