New research showed that a third of parents of Year Seven students across the country were unaware their teenager is eligible for free vaccines delivered at school.
The National Immunisation Program for high school starters includes three injections over six months, including three doses of the Human Papilloma Virus (HPV) vaccine, the "cervical cancer vaccine".
While the HPV was originally only offered to girls, it is now also available for boys.
Director of Communicable Disease at the NSW Health Department Vicky Sheppeard said boys were included on the HPV vaccination program two years ago after it was shown the virus could lead to genital warts and different forms of cancer in both sexes.
"There are other sites that the virus can cause cancer in men,” Dr Sheppeard said.
"The first visit is very important because with the HPV vaccine, students need to have three doses in specific timing. So it's really important to get your consent material back so that when our staff come to the first clinic your child is ready to be vaccinated.”
The immunisation program also includes other vaccines for diphtheria, tetanus and whooping cough.
If parents paid for the vaccines themselves, the three-dose program would be worth $450 per child.
Adolescent Physician at Westmead Childrens' Hospital Associate Professor Rachel Skinner said that while most parents return the consent forms in time, 15 to 20 per cent of students miss out on the free vaccines.
Associate Professor Skinner said consent forms often go missing or parents don't realise the importance of signing and returning them on time.
"For parents, it's a very safe way of vaccinating their children and very convenient way,” she said.
"These vaccines prevent life-threatening diseases. It's important that they (the children) receive these vaccines now, because we've worked out that this is the best time for the children to receive the vaccines, and to delay them increases their risk of catching these diseases."
Associate Professor Skinner said since the roll out of the HPV vaccine eight years ago, there had been a decline in the cases of genital warts and abnormal pap smears detecting pre-cancerous lesions in women.
"It is a remarkable vaccine,” she said.
“It has surprised even us how effective it is."
There had been some concerns, mainly in the US, that vaccinating girls against HPV would lead to increased sexual activity and unsafe sex practises. However, new research published in the Journal of the American Medical Association on Tuesday found no such link.
Dr Sheppeard said she's only encountered a small number of parents worried about vaccinations leading to sexually activity. She says in Australia, the importance of the vaccine is widely understood.
She said most parents know the vaccine is delivered in year seven because it is the optimal time for immunisation response.
If children do not want to be immunised at school, Year Seven students can still access the vaccines for free at their local doctor.
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