Bishop of Waterford and Lismore Phonsie Cullinan last week hit out at efforts to prevent the human papilloma virus (HPV) among women by saying "we have to do better than to give our boys condoms and our girls injections at the age of 12".
After being roundly criticised by the country's Health Minister and medical chiefs, the senior cleric issued a statement accepting that he had not been fully informed.
"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," he said.
Bishop Cullinan said he initially spoke out after parents had raised concerns with him about the HPV vaccine.
"My intention was solely motivated to protect people from the HPV," he said.
"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."
Health Minister Simon Harris had described the bishop's initial remarks as "ignorant".
The country's Health Service Executive, which has previously warned parents about conflicting and misleading information, said his criticism of the vaccination programme could endanger women's lives.
The HPV vaccine used in Ireland is Gardasil. It is said to protect against two high risk types of the virus, one of the most common sexually transmitted infections.
It prevents HPV 16 and 18, which cause 90% of genital warts, and is used in more than 25 European countries, the US, Canada, Australia and New Zealand.
Vaccinations against the HPV virus fell by half last year in Ireland amid scares over side-effects but the uptake has since stabilised.
Since 2010 more than 230,000 girls have been vaccinated, with about 1,000 reporting adverse reactions.
Most commonly, people fainted when injected or showed gastrointestinal symptoms, malaise, headache, dizziness and injection site reactions.
Other allergic-type reactions have been reported, including skin rashes, hives and flushing and isolated reports of more severe hypersensitivity-type reactions and some reports of persisting or chronic fatigue.
Ireland has one of the highest cervical cancer rates in Europe with more than 90 women dying from the disease every year and more than 280 others needing surgery, chemotherapy and/or radiotherapy.