Governors at St Monica's High School in Prestwich, Greater Manchester, have decided to not to allow its 12 and 13 year old pupils to have the cervical cancer vaccination.
The vaccinations give immunity to key strains of the sexually-transmitted Human Papilloma Virus, responsible for 70% of cervical cancers.
But the school's governors have written to parents questioning whether it is the best place to offer the course of three injections that have triggered side effects such as dizziness and fainting. The letter said: "We do not believe that school is the right place for the three injections to be administered. Therefore, governors have taken the decision not to allow the school premises to be used for this programme."
Monsignor John Allen, governor and parish priest, said: "This is not a moral judgment on the vaccination. It's a question of where this vaccination should be given and how it should be given."
Dr Peter Elton, Bury's director of public health, said he was respectful of the school's decision but disappointed that some girls may miss out on the vaccine as a result.
He said: "The vaccine will without doubt reduce the number of girls who contract cervical cancer later in life. We know that delivering the vaccination to girls aged 12-13 from a school setting achieves the best uptake.'"