The claim was first reported in Newsroom last week and relates to Mt Hobson Middle School, which is run by Villa Education Trust.
The student claimed a video was shown in a science class which purported to show that science had found proof of the existence of God.
The teacher at the centre of the controversy, Rachel O'Connor, is married to National MP Simon O'Connor and is the sister of Opposition Leader Simon Bridges.
Bridges did not respond to a request for comment.
According to Newsroom, the student who made the claims said creationism was taught as the preferred theory over Darwinism, with the latter referred to as an unproven theory.
He also said there was no discussion about the video before or after it was shown.
When asked for comment, Alwyn Poole, principal of Mt Hobson Middle School, directed EducationHQ to an interview with Mike Hosking on Newstalk ZB.
In that interview, Poole called the video “crap” and blamed the allegations on a disgruntled family.
He said that the family had raised their concerns about the video in 2016, and the school had communicated with them and “met [the family], we solved it and we moved on”.
Later, that same family was involved in a disagreement with the school over payment for house repairs.
Poole alleges the family had “sat on this for two years looking for an opportunity to have a crack at us” – and that crack came in the form of allegations of teaching creationism.
In the interview Poole denied that the school was teaching creationism as fact.
Darwinism, he said, is taught as an in-depth theory at Mt Hobson.
Mt Hobson Middle School states on its website that it “has a clear Christian philosophy and Christian values”.
Villa Education Trust also runs two government-funded charter schools, South Auckland Middle School and Middle School West Auckland.