Bishop Alphonsus Cullinan has apologised for "causing upset" with his comments on HPV vaccines.
Bishop of Waterford and Lismore had said last week that giving the injection to 12-year-old girls to guard against the human papilloma virus could lead to promiscuity.
"It's not only a medical issue, it's a lifestyle issue," he said. "It affects the lifestyle of our young people."
The Bishop added: "We have to do better than to give our boys condoms and our girls injections at the age of 12."
Vaccinations against the HPV virus fell by half last year amid scares over side effects but the uptake has since stabilised.
The Association of Catholic Priests yesterday asked the bishop to withdraw his comments.
The HSE said that he is endangering women's lives over his opposition to the vaccine and warned parents about conflicting and misleading information.
Bishop Cullinan said: "I wish to apologise for contributing to any misinformation, or indeed for causing upset to anyone, concerning use of the human papilloma virus (HPV) vaccines.
"My intervention was in response to concerns which I had received about HPV vaccines from parents wishing to make the best health decision on behalf of their children, and from young people alike.
"My intention was solely motivated to protect people from the HPV.
"I was not fully informed about the vaccination programme and I can see now how HPV vaccines can contribute greatly to lowering the rate of cervical cancer. As I have learnt, possession of full information is paramount on this vital health issue."