The roll-out of the vaccine to guard against cervical cancer poses a 'big logistical challenge' to primary care trusts, according to the Department of Health immunisation director.
Professor David Salisbury said immunising around 325,000 12-year-old girls each year against the human papilloma virus, which causes cervical cancer, is unlike other school vaccination programmes as it is a course of three injections.
He said: 'It will be a big logistical challenge for PCTs as the school-based programme needs three doses. It is not like other vaccinations and it will have to be juggled with the school term.'
The second dose is due a month or two months after the first and the final dose six months later.
He said PCTs must ensure records are kept to measure outcome.
Professor Salisbury added PCTs should foster links between the vaccine and cervical smear programmes to measure the impact of the autumn 2008 roll-out.
A catch-up campaign will start in autumn 2009: girls aged 16-18 years will be offered the vaccine from autumn 2009; and girls aged 15-17 will be offered the vaccine in 2010.
It is hoped the vaccine will save 400 lives a year and cut the number of abnormal smear tests, which can cause patients great anxiety.