Otago project leader Jo-Anne Skinner said families of the 53% of eligible girls had consented, which was similar to the rate around the rest of the country.
It had been hoped the rate might have been higher.
However, of the 29% who had declined at this stage, most of them were parents who wanted to defer vaccination or wished their daughters to have the vaccine at their family doctor.
A further 18% had not returned consent forms.
Mrs Skinner said regardless of the decision on the vaccination, it was important these were returned.
By the end of this week, 33 of about 57 schools participating will have hosted public nurses delivering 450 first doses of the three-dose vaccine.
Mrs Skinner said there had been no serious side effects reported so far.
Given the age group being vaccinated, it was expected that there could be some fainting, or "fainting by association".
It was vital girls had a good breakfast if they were scheduled for a morning vaccine, or lunch if they were being vaccinated in the afternoon.
`We do expect to have some fainting, sore arms and some people with headaches or feeling off. That's all perfectly normal with any standard vaccine."
Some year 13 girls have been vaccinated at schools visited by the 20 public health nurses on the programme, but Mrs Skinner said this year's school programme has been aimed at year 8 and 9 pupils, and older girls who wished to have the vaccine should contact their family doctor or Family Planning.
It is anticipated that next year the school-based programme would be broader to reach the the remainder of girls born after January 1, 1990.
At a glance
HPV vaccine
•Designed to protect against four strains of human papillomavirus (HPV).
•Two strains cause most genital warts.
•Two are linked to about 70% of cervical cancer.
•Vaccine considered most effective before a girl is sexually active.
•Girls who are sexually active still advised to have the vaccine as they may not have been exposed to all four strains.
HPV vaccination programme
•Will cost $177 million over five years and $16 million a year after that.
•Costs include, to schools participating in the programme, payments for every eligible girl.
•Will not replace the cervical screening programme, which costs at least $26 million a year.
•If about 70% of young women receive the vaccine, health planners say deaths from cervical cancer could eventually reduce by half to 30 a year.
