Up to 14 per cent of WA teenagers are not participating in a free vaccination program to prevent cancer and of those that do, thousands don't complete it.

Thousands of West Australian teenagers are missing out on protection against deadly cancers because they are not completing their full course of human papillomavirus (HPV) vaccine.

Between 12 and 14 per cent of year eight students did not consent to the free HPV vaccination.

Of those that did, 99 per cent - or 25,974 students - had the first dose, but only 97 per cent of females and 96 per cent of males had the second and only 90 per cent of females and 89 per cent of males the third.

The vaccine protects against two HPV types known to cause 70 per cent of cervical cancer in women.

It protects males from 90 per cent of HPV types that cause cancers of the penis, anus and throat, and against 90 per cent of genital warts in both sexes.

Studies showed more than 2500 students failed to finish the three-dose program last year, Health Minister John Day said.

"These numbers are concerning because they show that up to 10 per cent of participants are not getting the maximum protection," he said.

"The vaccine will help prevent cancer and disease later in life, and it is important that both students and their parents realise the value of completing the entire immunisation course."