The Australian Vaccination Skeptics Network posted an image of a woman holding his hand over her mouth with a caption claiming vaccinations are "forced penetration".
The image, posted on the group's Facebook page on Wednesday, has since been deleted.
The post prompted widespread outrage on social media, but spokeswoman Meryl Dorey said the group was not responsible for the image.
In a post on Facebook, Ms Dorey said that the page was "completely independent of the AVN".
"I agree that the image was very much in-your-face and should not have been posted here," she said.
The group also criticised media coverage of the image, stating "what standards is the media applying when they criticise someone for posting a meme comparing forced vaccination with rape?"
The group has compared vaccination to rape in the past.
In a tweet four years ago, the group compared a court ordering the vaccination of a child as court-ordered "rape".
The overwhelming majority of scientific and medical evidence supports the benefits of vaccines. In 2014, a major international review found no evidence linking the development of autism with commonly-used vaccines for measles, mumps, rubella, diphtheria, tetanus and whooping cough.
In March last year, the Australian Vaccination-Skeptics Network lost its charity status over concerns it could adversely affect children's health. The group was also forced to insert the word "skeptics" into their name over claims their title was misleading.
