HSE officials say the benefits of the injection far outweigh the risks
Parents have been urged to review scientific evidence on the HPV vaccine after a drop-off in uptake rates.
Provisional statistics from the HSE show that 70% of eligible schoolgirls received the injection in 2015-16, compared to 87% during the previous academic year.
Dr Brenda Corcoran of the HSE's National Immunisation Office described the figures as a significant cause for concern.
"It means around 5,000 girls who would ordinarily have been vaccinated missed out last year," she told Newstalk.com.
The vaccine, which protects against cervical cancer, has been offered free of charge to girls in their first year of secondary school since 2010.
The jab is recommended by the World Health Organisation (WHO), the National Immunisation Advisory Committee and the International Federation of Obstetricians and Gynaecologists.
Some parents have claimed, however, that their children suffered severe side effects following the injection.
Dr Corcoran said that those with reservations about the vaccine should carefully consider the source of their information.
"The major reason [for the fall in uptake] is that parents are concerned about safety," she told Newstalk.com.
"There have been a number of stories in local, national and social media claiming it causes serious adverse effects.
"Parents are seeing that information and taking it as fact."
Dr Corcoran insisted that there was "absolutely no evidence" linking the vaccine to illnesses cited by some parents.
She said reported long-term side effects occur with the same frequency among vaccinated and unvaccinated girls.
"Our message is that HPV causes cancer. This vaccine is safe and prevents cancer in later life," she said.
"If parents choose not to allow their children to get the vaccine, they may go on to develop cervical cancer."
An estimated 300 women are diagnosed with cervical cancer in Ireland every year, with 90 women dying from it, according to the HSE.
Dr Corcoran advised parents and guardians of first-year schoolgirls to read WHO-accredited information on the HSE website.
She added that officials were conscious of the need to improve its communication strategy, describing the process as one that "takes time".
But vaccination teams and local health service staff are already working hard to provide parents with the relevant scientific evidence, she said.