"The ad was basically about being smoke free. Our house is smoke free so that I can have a better future for my girls," he told 3News.
The footage was shown to health groups, including La Leche League and Plunket, for feedback.
La Leche League director Alison Stanton told the Herald on Sunday the trouble was not with Weepu bottle feeding but with the overall message.
"It's really important that those messages are consistent across the board. It's been resolved and was really a storm in a tea cup."
Karen Guilliland, chief executive officer of the College of Midwives, told the paper the organisation also opposed the ad too. "We just figured that Piri Weepu was so loved that whatever he did would carry a huge weight."
However the decision to cut the footage has been widely criticised, with some pointing out men and many women cannot breastfed.
"I'm pretty sure a lot of dads would like to be more hands on, but when it comes to feeding babies we don't have that luxury," Weepu said.
"They are my kids, I'm not going to have anyone tell me how to raise me kids."