Bishop Pat Storey said many are now unable to afford an Anglican education for their children.
In the Republic most Protestant schools are private and fee paying.
The country's first female bishop said people find the "economic situation very difficult".
Parents were finding it "harder and harder" to pay for the fees, she told the Belfast Telegraph.
She said that Church of Ireland parents would now have to send their children to state schools, many of them would be Catholic.
"I think we have to be broadminded enough to provide different provisions for different faiths and non-faiths so that people can step out of religious education class or confirmation preparation if that is not for them," she said.