The couple are said to be "upset" with the publication of the images, the Daily Mail said.
"The Duke and Duchess of Cambridge considered their honeymoon to be a very private event after their hugely public wedding, a St James's Palace told the paper.
"For this reason they asked the media to respect their privacy. That is something they continue to do so."
The magazine's Facebook page has already been hit by angry reaction.
"Shame on you woman's day for printing those photos of William and Katherine ....everyone deserves to have private time ..." Sarah Waite wrote.
"They gave us great wedding photos you should have left it at that."
Marie-Louise Burness agreed.
"That was William's and Catherine's private honeymoon. I really hoped that the media, especially Australia's media, would have had some respect for the couple, after all what Princess Diana went through. I remember the late princess saying once that she didn't mind the media when it involved her charities. I'm sure we would survive without seeing such private and intimate photos."
The page's administrator said the magazine values reader feedback and would be passing on their comments to the team.
The incident is not the first time an Australian publication has raised the ire of the royal family. In 2008, New Idea broke a similar media agreement by publishing the fact Prince Harry was serving in Afghanistan.