An investigation by GP magazine found that 15 PCTs out of 83 that responded to a Freedom of Information request had one or more schools refusing to take part in the HPV vaccination programme.
More than 24 schools across the 15 PCTs had opted out, in many cases on the grounds of religious faith. Opt-outs could become more common because academies and free schools being rolled out by the government have greater freedom from local authority control.
Of the 15 PCTs with schools that opted out, only two said they informed GPs. Nine PCTs admitted they did not tell GPs and for a further four it was unclear if GPs were informed.
Only five PCTs said pupils or guardians were notified of how to obtain the vaccine elsewhere.
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GPC deputy chairman Dr Richard Vautrey said: 'It is a concern that so many areas are reporting that schools have refused to allow their children to receive HPV vaccine on the premises. This is placing their children at risk in later life and should be challenged.
'It is also a concern if PCTs are not informing practices about HPV uptake.'
RCGP immunisation spokesman Dr George Kassianos said GPs must be told who has been denied vaccination at school to reduce rates of cervical cancer, which claims around 1,000 lives a year in the UK.
Dr Kassianos said: 'If GPs are going to be provided with vaccines and there is an agreement that GPs can vaccinate those falling behind, then it is even more important that GPs are informed about who has missed HPV vaccination at school.
'GPs also need to know of completion of vaccination courses.'
Dr Vautrey said that when councils take on public health responsibility next April, closer links between public health and education departments should make this 'failure to protect our children' less likely to occur.
He said this would not prevent academies or free schools opting out of vaccination campaigns in future. But he added: 'It would put more pressure on them if all other schools were offering this.'
Dr Kassianos called on academies and free schools to take part in school immunisation programmes.
He said: 'They have a public health responsibility to improve children's health.'