National leader Simon Bridges says there's no evidence that his sister taught creationism as a preferred theory of evolution in science classes.
Mt Hobson Middle School teacher Rachel O'Connor is at the centre of the allegations - she is Mr Bridges' sister and wife of National MP Simon O'Connor.
One of her former students, who has not been named, told Newsroom his Year 10 class was shown a video in 2016 called 'Science Has Found Proof of the Existence of God'.
"I respect anyone's religious beliefs, I have no problem with that, but this is a science class," the student said.
The school is one of two private schools run by the Villa Education Trust, which also operates two charter schools.
The student's mother, a trained secondary teacher, told Newsroom that showing the video in a science class amounted to "slick Christian propaganda".
"The reality is, this wouldn't be a story if it wasn't my sister," Mr Bridges told Newshub.
"It is a political hit job. We have got here a christian private school, there's nothing wrong with that we live in a free society we can have these sorts of things, and to the best of everything I've seen, to my knowledge, they're following the curriculum."
Mr Bridges said he believes in evolution.
"I think that natural selection and so on has been proven to be the case. I also have a Christian faith."
Mt Hobson Middle School's academic manager Alwyn Poole told RNZ he stands by Ms O'Connor, and disagrees with the student's claims.