The Health Service Executive has confirmed that the number of students who received a first dose of the HPV vaccine fell from 80% in 2019, to just 53.6% in 2020.
Just 37,014 of 69,111 First Year students were vaccinated last year.
The figures were obtained by Labour Leader Alan Kelly through a series of parliamentary questions.
HPV (human papillomavirus) causes a number of cancers including cervical, oropharyngeal, anal and penile cancers.
Since September 2019, the vaccine has been given to boys and girls in their first year of secondary school.
In a statement, the HSE said that "for most of this year's first year students, they will be offered their vaccines in a clinic arranged by their school vaccination team later on this year.
"Any first year students who were due the HPV vaccine but didn't get it due to the impact of the COVID-19 pandemic will still be offered the vaccine.
It said that it looks "forward to being able to offer a full programme of school based vaccinations when the risks associated with COVID-19 rates in our community have reduced."
Earlier this year, the HSE said that the School Immunisation Programme, which includes the HPV vaccine programme, was "paused as school teams are now giving the Covid-19 vaccine."
It added that "contact would be made with parents and guardians when the programme restarts."
Campaigner and patient advocate, Stephen Teap, had called for a "clear timetable and plan put in place" by the HSE "to catch up on the HPV vaccination programme.
There needs to be a clear timetable and plan put in place by the @HSELive to catch up on the HPV Vaccination program, no more "covid" excuses. Protect Laura Brennans legacy, get this done now and save lives of future generations from HPV.@DonnellyStephen— ?????????????? ???????? (@Stephenteap) March 27, 2021
The HSE said that "school closures and the redeployment of school vaccination teams to Covid-19 vaccine roll-out have interrupted school vaccination programmes."
It said that when schools reopened last September, many were "unable to facilitate" vaccination teams "due to the Covid-19 pandemic."
It said that "as many students as possible" were facilitated in schools "where vaccinations were permitted", and in clinics outside of schools "where possible".
"A very limited number of school teams have been able to restart clinics for school vaccinations," it added.
No information on the number of children vaccinated in 2021 was available from the HSE.
"As the programme is ongoing, uptake information is not available", the statement said.
On the second anniversary of the death of Laura Brennan, who campaigned to promote the HPV vaccine, her family issued a statement expressing their "concerns regarding the deferral of this year's roll out..."
The family appealed directly to the Department of Health, and asked it "to review its current HPV vaccine administration plan and increase its efforts to protect our future generations."
The HSE said that "maintaining high uptake of the HPV vaccine and honouring the legacy of Laura Brennan and her work with us is very important to everyone in the health service."