The three-dose human papillomavirus (HPV) vaccine protects against 70% of cervical cancers and 90% of genital warts.
The program was introduced in Australia five years ago as part of the national immunisation program.
Girls aged 12 to 13 across the country have been provided the vaccine free at school since 2007.
But Cancer Council Victoria (CCV) figures show only 76% of girls in Victoria are having all three doses of the vaccine under the school-based program.
CCV cancer screening programs manager Kate Broun said girls were not having the full dose because of barriers including pain, fear of needles and lack of understanding about what the vaccine is for.
"Taking all three doses of the HPV vaccine is the best step young teenage girls can take to reduce their risk of cervical cancer," she said.
"By following this up with regular pap tests once they're older, they are significantly decreasing their risk of developing the disease."
CCV has released a new online video explaining the vaccine in a bid to encourage further uptake among teenage girls.
Research shows that in the five years since the school-based HPV immunisation program was launched, the number of girls under 18 with high-grade abnormal pre-cancerous cells on the cervix has halved.
High-grade abnormalities, usually caused by the HPV, can develop into cervical cancer if left undetected and untreated.