A battle over how many women will qualify for the cervical cancer vaccine on the NHS began yesterday as the Government announced routine immunisation of all schoolgirls aged 12 to 13 would be introduced next September. A catch-up programme for girls aged up to 18 will start a year later. But girls who have left school by autumn 2009, who are now aged between 16 to 17, will not be covered by the initiative.

The announcement follows a recommendation by the Joint Committee on Vaccine and Immunisation (JCVI) that the newly licensed vaccine could save hundreds of lives a year. It protects against human papilloma virus (HPV) and trials show it can prevent at least 70 per cent of cervical cancers.

The vaccine is most effective if given before sexual activity starts, but evidence shows it may still be of benefit to women aged 25 and older, depending on their level of sexual activity and exposure to the virus. Studies show 25 per cent of women of university age are infected with HPV – suggesting up to 75 per cent may still gain protection from the vaccine.

Most women infected with HPV clear the virus quickly, but in some it becomes chronic, and can cause changes in the mucous membrane of the cervix, leading to cancer up to 20 years later.

Levels of HPV infection rise steeply from the start of sexual activity in the teens, peaking in the twenties. Over a lifetime, 80 per cent of sexually active women will be infected.

Professor David Salisbury, the head of the Department of Health's vaccination programme, said the trial results for the vaccine were "fantastic", with only minor side-effects and strong indications protection would be long lasting. "They show it is possible to change the course of cancer. It is very exciting," he said.

Asked if there was any possibility the vaccine would eventually be made available to girls now aged 16 to 17, Professor Salisbury said: "This is an issue we have got to negotiate – what advice we are going to give and how GPs should deal with requests for vaccination. We have not got an answer yet."

He urged parents of older girls not to rush to get them vaccinated privately. "The vaccine is not effective in sexually active girls once they are infected. My advice to concerned parents would be to wait. We want to advise GPs how to answer this question."

Private clinics are offering the new vaccine for up to £500 for a course of three doses, and doing brisk business among women in their teens and twenties.

Pamela Morton, of Jo's Trust, which has campaigned for the introduction of the vaccine, welcomed the Government's announcement, but warned about the exclusion of 18- to 26-year-olds.

"These women will continue to be exposed to the dangers of HPV," she said. "The JCVI and the Government should act now to offer all women up to 26 the opportunity to self-refer to their GP and receive the vaccine free of charge."

Two cervical cancer vaccines are licensed, Gardasil, made by Merck, and Cervarix, made by GSK, and a bidding war for the government contract is expected to bring the price down from its current £300 a course. Only one vaccine is likely to get chosen for the programme.

The chief executive of Cancer Research UK, Harpal Kumar, said: "This is an exciting step towards preventing cervical cancer in the UK."

But he warned: "While the vaccine has the potential to prevent many cases of the disease, the impact of a vaccination programme is unlikely to be felt for many years."

Decision that will save women's lives

How common is cervical cancer?

There were 2,221 cases diagnosed in 2004. There were 831 deaths in 2006.

What causes it?

Ninety-nine per cent of cases of cervical cancer are caused by infection with human papilloma virus, which also causes some other genital cancers and genital warts.

What does the vaccine do?

It protects against two strains of HPV – 16 and 18 – which are the commonest causes of cervical cancer accounting for about 70 per cent of cases.

The remaining 30 per cent of cases are caused by other types of HPV which are not included in the vaccine. The vaccine is expected to save 400 lives a year.

How effective is the vaccine?

Very. It is 99 per cent effective in protecting against HPV strains 16 and 18. Studies show the protective effect is likely to be long lasting – for 10 years, 20 years or life – but experts said they could not rule out the possibility that women might need a booster jab in the future.

Is it safe?

No evidence of serious side-effects has emerged in the trials and there is no evidence it causes harm when given in pregnancy. Minor side-effects of redness, pain and swelling at the site of the injection are common. The vaccine is given in three doses over six months.

Will cervical screening still be necessary for those who have had the vaccine?

Yes. The vaccine protects against 70 per cent of cervical cancers, but there is still a 30 per cent chance of developing the cancer. Also, if a teenager is sexually active and infected with HPV when vaccinated, the vaccine may have no effect.

Is it worth vaccinating young women aged 18 to 26?

The Government says it is not cost effective because many of them will already be sexually active and infected with HPV. But for women who are not sexually active and not yet infected with HPV, vaccination will be protective in the same way as for younger girls.

Even in women who have been infected and have cleared the virus naturally, vaccination may still be protective, although scientists are undecided about this.

Should parents pay the £500 cost to have their older daughters, who will fall outside the NHS scheme, vaccinated privately?

Professor David Salisbury is not keen. But Dr Anne Szarewski, of the Wolfson Institute, London, who conducts research into HPV, said: "If you can afford it, it is well worth doing, though there is no guarantee of protection."