Schoolgirls across the UK will be offered immunisation against genital warts, one of the most common sexually transmitted infections, in a move welcomed by doctors.

It will expand the existing vaccination against cervical cancer for 12- and 13-year-olds.

The change will take place at the start of the next school year in August and September 2012. All 12- and 13-year-old schoolgirls will be offered a vaccine called Gardasil, which protects against the two strains of the human papilloma virus (HPV) that cause 70% of cervical cancers and also two other strains that produce 90% of genital warts.

It will replace Cervarix, which has been used since immunisation began in 2008 but only offers protection against cervical cancer.

The drive against HPV has been successful. Latest official figures show that 77% of 12- and 13-year-olds, and 84% of 14- and 15-year-olds, have voluntarily received the full course of three HPV jabs, either at school or at their GP's surgery – the highest uptake in the world.

Ministers have decided to make the switch after advice from their independent advisers, the Joint Committee on Vaccination and Immunisation, and studying evidence collated by the Health Protection Agency.

About 75,000 people a year in England are diagnosed for the first time with genital warts, but the total number of those developing it annually in the UK is around 161,000 people, once those who find that it has recurred despite treatment are included.

Professor David Salisbury, the government's director of immunisation, said the switch had been made after examining new evidence from Australia where Gardasil had greatly reduced cases of genital warts among both girls and boys while preventing the same number of deaths a year from cervical cancer as Cervarix, estimated at 400.

"We looked at the science and we looked at the price. We have reflected the changes in scientific knowledge that has become available since last time. They are not huge changes – we still prioritise the prevention of cancer – but based on all these things the winner is Gardasil," said Salisbury.

Dr Peter Greenhouse of the British Association for Sexual Health and HIV said the organisation was delighted by the news. He said that if 70% of girls continued to be immunised against HPV, "we should expect to see genital wart infections start to reduce in teenage girls within five years, and slightly later in boys.

"If we continue to vaccinate just 70% of 12- to-13 year-old girls, we can predict that genital warts should be eradicated in heterosexual women and men within 20 years, through the herd immunity effect," he added.

Greenhouse said Gardasil should be made available to young gay men on their first visit to a sexual health clinic in order to protect them against anal and oral cancers as well as genital warts.

The Aids charity the Terrence Higgins Trust also welcomed the decision because "it makes sense in terms of improving women's health and will also save the NHS millions."

But the charity called on ministers to offer the vaccine to all boys to protect them against some male cancers.

A British Medical Association spokeswomen said: "The latest evidence shows that Gardasil has superior public health benefits and is more cost effective.:

Dr Tony Falconer, the president of the Royal College of Obstetricians and Gynaecologists, said: "The quadrivalent vaccine will also protect against the strains of HPV that cause genital warts, which are unpleasant and the cause of much psychological distress for sufferers."

The Health Protection Agency said: "Warts are a common sexually transmitted infection in the UK, and as a result of this decision we expect to see a reduction in the number of diagnoses over time."

"We understand that the choice of the quadrivalent vaccine [Gardasil] in the UK followed a competitive tender. This tender was informed by a detailed scientific study comparing the two available vaccines against a range of criteria, including scientific qualities and cost effectiveness."