Health Minister Dr Jonathan Coleman welcomed the funding decision.
"The [HPV] vaccine will be changed from a vaccine that protects against four HPV serotypes to one that covers nine. The change increases protection against cervical cancer from 70 per cent to 90 per cent.
"These changes will mean the number of doses required for 14 year olds and under will be reduced from three to just two."
In Australia, the HPV vaccine is government-funded for boys and girls. Gardasil can protect against four strains of HPV - human papilloma virus - that can cause pre-cancerous lesions in the genital tract and mouth, and genital warts. It has been offered to New Zealand girls partly to help reduce cervical cancer.
Rates of throat-related cancers have risen sharply since the 1980s and HPV, from oral sex, is thought to be the cause.
More than 200,000 New Zealand females have received the vaccine since 2008.
Other changes to the currently listed vaccines including brand changes and a move to a 2-dose schedule for vaccination against rotavirus.
May's Budget boosted Pharmac's budget by $124 million over four years. The Government said DHBs would also give an extra $11 million towards Pharmac's budget next year.