Another person commented: "OMG they definitely didn't choose the cutest bubs."
The comments could no longer be found on the Bonds' Facebook page today.
Many people slammed the critical comments as "nasty" and "vulgar".
"All babies who entered this competition are beautiful, whether they win or not," said one.
Another commenter hit out at the competition itself, writing: "Don't complain if people are judging your kids harshly. You the parents are to blame for subjecting your kids to this."
Bonds' spokeswoman Emma Street said the company was very disappointed with the comments of a few parents.
"All the baby's [SIC] are beautiful and we have a very difficult task to select the ones we feel have that special Bonds energy in their photographs - after all they need to represent our brand in the market place.
"It's simply not acceptable that the comments of so few ruin the celebration for the 15 winners and all the families that entered their beautiful babies."
The company did not say whether it removed any offending comments, but said people could "express their opinions freely".
Previous years of the competition have also been marred by negative comments about the entrants.
More than 60,000 people entered the contest this year. The winning babies have the chance to become the face of Bonds' baby clothes campaigns, while the parents receive Bonds vouchers and a framed photo of their child.
Two of the 15 winners were babies with Down Syndrome, Australian parenting site Mamamia reported.
Sarah Kiss, the mother of winning baby Ruby, who has Down Syndrome, said: "I hope everyone can see that everyone should be treated equally and everyone is beautiful no matter what."
