The Catholic Church originally raised objections to the jab on the grounds it could encourage promiscuity, but has made a U-turn after reaching an agreement with health and education bosses.
The deal means girls getting the HPV jab will not receive any accompanying advice on the need to use condoms to protect themselves from other sexually transmitted diseases.
Health campaigners and parents' groups last night reacted angrily to the deal, warning that the sexual health of thousands of young Scottish women was being put at risk to avoid a moral backlash from the Catholic Church.
Many sexual health experts believe it is essential to give out safe sex advice alongside the jab to make it clear they will remain at risk from other STIs including HIV, chlamydia and gonorrhea. More than half of the 5,000 female chlamydia patients in Scotland last year were under the age of 20.
The vaccine has been shown in trials to be highly effective in stopping cervical cancer caused by HPV if given to girls before they start sexual activity. Such cancers account for about 70% of cases of cervical cancer, which claims about 100 lives in Scotland every year.
When the decision to give the jab was announced by ministers in August 2006, a spokesman for Cardinal Keith O'Brien warned it could be seen by pre-teenage girls as a "green light" for sexual activity.
The programme is due to start next month and schools are set to send out consent forms for the scheme from the beginning of September.
The Catholic Church has now decided it will back the programme, with the jabs being available in its own schools.
Spokesman Ronnie Convery revealed: "We have been in fruitful discussion with the health and education authorities, and we are satisfied that the programme to be rolled out across the country now is a responsible and ethically appropriate one."
Director of the Scottish Catholic Education Service (SCES) Michael McGrath added: "We wanted to make sure any support materials were appropriate in the Catholic schools, and we didn't want HPV and cervical cancer to be linked with artificial contraception. The factual information about the vaccine and cervical cancer are still there, but it doesn't promote particular kinds of sexual behaviour. We had discussions about it, we looked at various forms of words and came to an agreement. It took some months."
A spokeswoman for the Family Planning Association (FPA) said it was a missed opportunity. Chief executive of the FPA Julie Bentley said: "The HPV vaccination will only protect young women from two strains of HPV leading to cervical cancer. It is critically important that young people understand the need to use condoms to protect them from other STIs."
Scotland Patients' Association chairwoman Margaret Watt said: "This message should be highlighted and underlined – please remember this injection doesn't protect you from sexually transmitted diseases or becoming pregnant."
Justine Roberts, co-founder of Mumsnet, said parents would be annoyed by the omission. She said: "The moral position is being imposed upon them. It seems a bit archaic to let the Catholic Church decide on this."
A Scottish Government spokesperson said: "The HPV vaccine is about saving lives and protecting future generations of young girls from cervical cancer.
"Scottish Government officials consulted with many stakeholders and undertook research with parents and girls to ensure the right level of information was included in the leaflet. The Scottish Government is absolutely committed to promoting safer sex, and we are taking forward our sexual health strategy 'Respect and Responsibility'."
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