The North & South piece has sparked a highly charged debate - but about the cover, not the content. The cover emblazoned "midwives" in pink and yellow capitals over a naked, crying baby held upside-down.
The image sparked widespread condemnation on Facebook and an angry press release by the College of Midwives.
Dr Wills, a former head of the paediatrics department at Hawkes Bay Hospital who began as Children's Commissioner on July 1, last week lodged his formal complaint with the Press Council, which oversees ethical standards for print publications.
"In my view the image is not 'bold', but grotesque and potentially harmful.
"The image does not represent the values New Zealanders have towards children. The image is degrading and exploitative," Dr Wills said.
He pointed out that reporting guidelines issued by the International Federation of Journalists called on publications to "avoid the use of stereotypes and sensational presentation to promote journalistic material involving children".
North & South editor Virginia Larson said the photo had been sourced from a reputable agency - Getty Images - with a robust code of ethics, and she was confident that no child was harmed in the photoshoot.
The cover did not depict childbirth literally - it was a concept to pull readers into the story by getting attention "on a crowded newsstand", she said.
"Would a New Zealander seeing the cover somehow be incited to harm a child? I just have difficulty making that connection."
The response by the Children's Commissioner surprised her, Larson said.
"Maybe he's new in the term - he's got a five-year term - and he's feeling he has got to push this.
"If government agencies are now going to police cover designs, where do we go from there?"
She noted that most of the Facebook postings began "I haven't read the article but ..."
