He and project manager, parishioner Peter Jeffs, sought a discount because of the church's charitable work in the community.
"We're a charity that does a lot of good in the community and given that our society depends so much on charities, it's disappointing. When things go wrong in life it's my door, and other priests' doors, that get knocked on.
"We don't want to be made out to be scrooges and I totally respect that it costs something [to process consent applications], but should charities be expected to pay the full amount?"
Council spokeswoman Angela Jones said the council was bound by the Resource Management Act, which required consent applicants to pay, rather than ratepayers.
The council would honour agreements made by previous greater Auckland councils before amalgamation, such as a fee waiver for charities agreed to by the former Rodney District Council. The waiver would continue until the district plan was changed.
However, she offered some hope for Baxter and his parishioners, noting the cost of the consents was an estimate and could fall if fewer inspections were needed.