Suzanne, not her real name, did not know her daughter was sexually active before her husband discovered the pills in her daughter's school bag.
It is really hard to get your head around the fact that when your child goes on an excursion they need to have a permission slip signed by the parent, but the school is within its rights to take a child to the doctor to be put on the pill," she told Geelong Advertiser.
Bellarine Secondary College principal Colin Sing defended his school, saying staff were bound to protect students' welfare and privacy.
It is the second time in two years the school has been embroiled in such controversy. In 2006, a Leopold mother complained she could not stop the school's nurse helping her daughter get a contraceptive implant.
Sing conceded privacy regulations could be at odds with parents' wishes.
"In cases that involve health professionals, there are even more stringent regulations in relation to protecting the privacy of students in their care," Sing said.
"Where a student is deemed at serious risk or there is imminent threat to the student's health and safety, the student can be referred to a general practitioner."
Suzanne said the school nurse encouraged her daughter to talk to her mother about having sex but she chose not to.
"Had she come to me and said, 'Mum, I want to go on the pill', I would have been able to talk to her about it and be in control, I would have been able to take her to my family doctor and make sure she was properly educated about it," she said.
"She didn't even know how to use the pills properly."
Suzanne said she was now organising a sex education session for her daughter through a health clinic.
"Just what exactly am I entitled to know? My daughter needs real education on relationships and sex and she is not mature enough to make that decision alone,'' she said.
"All these privacy regulations do is break down the relationships between parents and their children.''
Sing said it was up to a GP to decide whether a student should be prescribed the pill, not the school's wellbeing co-ordinator.
"These issues are very uncommon in our school considering we have more than 1200 students. The problems that underlie these student health issues are very complex and generally family related,'' Sing said.
A spokeswoman from Medical Indemnity Protection Society medico-legal advisers said doctors assessed whether a young person was capable of giving consent to medical treatment but age was not a factor.
Doctors and school nurses are required to protect confidentiality if, in their judgment, a student is capable of making sound decisions.
The society uses British common law as the basis of its advice, which says that young people can make decisions about their lives and bodies if they have a mature appreciation of the issues. These views have not yet been tested in Australian courts.
Sexual health expert Dr Sally Cockburn said it was sad the girl felt she couldn't discuss her health with her parents.
"We need to look at why kids feel they cannot talk about this with their parents," she said.
"If she had and the parents refused to give her the pill it's not necessarily going to stop her having sex.
"I worry more about the kids at this age who are having sex and not seeking contraception." Dr Cockburn said the nurse had not done anything wrong and had acted withing her duty of care to the girl.
She said it was more an ethical question for doctors about whether the pill should be described at that age without parental consent, but that children under the age of 16 didn't need consent from their parents if they were deemed a mature minor by the doctor and and able to make their own decisions.