Minister for State at the Department of Health Finian McGrath has told RTÉ News that he supports the HPV vaccination programme.
But he said he will continue to raise the concerns of parents about the vaccine.
He confirmed that he spoke to Health Minister Simon Harris and he strongly supports Minister Harris' position that parents should follow medical advice.
But he added that as an Independent member of the Oireachtas, it is his duty to challenge decisions and there is nothing wrong with him raising concerns that parents asked him to raise.
Earlier this week, the Health Service Executive launched a campaign aimed at encouraging parents to have their daughters vaccinated to help prevent cervical cancer.
Uptake of the vaccine is currently at an all-time low, having dropped from 90% to 50% last year.
The drop follows claims that a number of girls have suffered serious side effects from the injection.
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Yesterday, Mr McGrath acknowledged: "On the issue of the HPV vaccine, I did raise concerns about it when in Opposition last year. I stand over the fact that I raised it because concerned parents asked me to raise it.
"Parents have a right to voice any concerns they have relating to vaccines or any form of medication being introduced for their children.
"Personally and as Minister of State with responsibility for Disabilities, I do accept that such vaccines are a very important part of Government health strategy."
Mr Harris yesterday said he had spoken to his Government colleague.
In a statement the Department of Health said: "Minister McGrath assured Minister Harris that he supports the new campaign to encourage parents to avail of the HPV vaccine which saves lives and he welcomes the fact the whole purpose of the new campaign is to help inform parents and direct them to medical professionals to have any questions answered and facts provided.
"Ministers Harris and McGrath agree that the people qualified to give advice on vaccines are medical professionals and they would encourage parents to take advice from them.
"Minister Harris said ‘the HPV vaccine saves lives and my appeal to parents is simple - get the facts and information from medical experts. Talk to your doctor. Check out HPV.ie'."
Irish Cancer Society raises concerns over McGrath comments
The Irish Cancer Society has called on Mr McGrath to publicly clarify his support for the vaccination programme.
"While the Society welcomes Minister Simon Harris’ intervention in the matter, a unified approach from all Ministers is required to ensure the uptake rate of the life-saving HPV vaccine is increased and to ensure misinformation about the vaccine is dispelled," said the Society in a statement this evening.
"This is why Minister McGrath needs to take responsibility, as a Minister in the Department of Health, and publicly make clear his full and unwavering support for the national HPV Vaccination Programme."
"The HPV vaccination is safe and has been proven to save lives.
"Research by multiple independent, international experts analysing the 80 million vaccinations administered to date has found no difference in the rates of serious illnesses between vaccinated and unvaccinated individuals," added the statement.