The vaccination targets the strains of Human Papilloma Virus which cause up to 70% of cervical cancer in women each year.
Southland PHO registered nurse Katrina Grant, of the HPV immunisation team, said the take-up of the vaccine had been very good across Southland and Wakatipu.
On Friday, about 70 female pupils from years 8, 12 and 13 were given the first of three shots.
The other years would be targeted next year, Ms Grant said.
"It is a year 8 programme and after that it will carry on from there."
All schools in the Southland District Health Board region had been invited to be a part of the immunisation programme - in Wakatipu, Glenorchy School, Arrowtown Primary School and Wakatipu High School had taken up the invitation.
Ms Grant said there had been a "very positive reaction" to the programme and the team of nurses would be back for a second round of injections in two months.
After that, there was a four-month stand-down before the third and final jab, which would be given in August or September.
The immunisation programme will not eliminate the need for women to have regular cervical checks because the vaccine does not cover some forms of the HPV virus which can cause cell damage and lead to cervical cancer in some women.
"The two programmes will run hand in hand," Ms Grant said.
Women over 18 and under 26 could pay for the vaccine, which was available through doctors and health-care providers.
It is free for girls under 18 and born after January 1, 1990.
Those who miss out on the school vaccination programme are able to get it through their GPs or Family Planning.
