Less than a third of New Zealand schoolgirls have received the controversial cervical cancer vaccine, as health concerns persist around the $177 million programme.

The Labour Government launched the Gardasil programme in September last year, with the aim of immunising 300,000 Kiwi schoolgirls over the next two years.

Latest figures show 26 per cent of 12 to 16-year-olds and 35 per cent of 17 and 18-year-olds have received the first of three Gardasil doses.

One advocate conceded the numbers are "very low".

The introduction of Gardasil has not been without controversy. Some accused the Ministry of Health of rushing an expensive vaccine programme of which the effectiveness had not been proven. Concerns from religious groups have centred on the fact the vaccine protects against a virus that is sexually transmitted.

The vaccine is most effective if administered before sexual activity begins, which is why girls as young as 12 are the focus. Some parents fear this will encourage sexual promiscuity.

Christy Parker, policy analyst for Women's Health Action, said the trust was concerned that Gardasil had been marketed as "the cervical cancer vaccine" when it doesn't protect against all forms of cervical cancer, and fears it may undermine the importance of three-yearly cervical smears.

"The relationship between the HPV virus and cervical cancer is complicated," she says. "We're concerned that when we have a generation of young women who believe they've had the cervical cancer vaccine ... we might have a generation who don't participate in the cervical screening programme."

Dr Nikki Turner, director of the University of Auckland-based Immunisation Advisory Centre, agreed there was a risk the importance of cervical screening may be undermined by Gardasil. "But I don't think that's an argument to stop preventive care."

Turner conceded the numbers of girls and young women having the vaccine so far have been "very low". "But I also think that because it's not a mass epidemic problem, it takes the community a while to understand this virus and the vaccine."

Dr Greg Simmons, the Ministry of Health's chief adviser for population health, said: "We recognise this is a new immunisation for New Zealand and some parents may be taking a wait-and-see approach."