Peters was answering questions from an audience when the unidentified man asked "where is your evidence that there is a virus that causes this disease"?
"Here's someone who gets up and says 'the Earth is flat'," Peters responded. "Sorry sunshine, wrong place."
New Zealanders go to the polls on Saturday (October 17).
Peters was a kingmaker in the country's previous election, siding with the Labour Party leader Jacinda Ardern to form a coalition government.