Health Sponsorship Council chief executive Iain Potter said the camera followed Weepu around for a day, including for an hour at his home while he played with his daughters.
"He happened to feed the 6-month-old briefly while they were there," Potter said. "It was a nice little poignant moment but we understand the sensitivities around it."
Potter consulted La Leche and Plunket about the clip.
"While we know breast is best, we weren't quite sure what people would think about it. So we canvassed expert opinion."
People associated with the La Leche League initiated an email campaign against the ad, resulting in a "significant amount of feedback" to the council.
"It was important for us that people understood the key message of the ad was about smoke-free air for our kids. We didn't want that to get lost in a controversy around bottle-feeding."
La Leche League director Alison Stanton said the trouble wasn't 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."
Asked what was wrong with Weepu cuddling and feeding a baby, she said: "You've got the healthy eating message, exercise, breastfeeding, smoke-free environment, wearing safety belts and this is about making sure that we give consistent health messages."
Weepu said he was trying to encourage non-smoking.
"I started doing the campaigns last year and wanted to be involved again because I think it's doing something good for the community. I wanted to set a good example and make a better future for my children."
Karen Guilliland, chief executive officer of the College of Midwives, said her organisation opposed the ad too. "We just figured that Piri Weepu was so loved that whatever he did would carry a huge weight."
