A free meningococcal vaccine will be provided to teenagers aged 15 to 19 in WA after a "disturbing" increase in cases of the W strain, and the health minister hopes the rest of the nation will follow the state's lead.

The vaccination protects against the potentially deadly meningococcal strains A, C, W and Y and will be rolled out in term two and three of this school year.

Health Minister John Day said the incidence of the W strain had been rising since 2013, but jumped from four in 2015 to 14 last year, compared to three cases during the four-year period to 2014.

"The advice we've had is that it would be preferable for this vaccination campaign to be undertaken on a national basis," he told reporters on Sunday.

"We have been in discussions with the Commonwealth ... the issue is still under consideration.

"We are starting on a state-wide basis, we do hope that other states and the Commonwealth ultimately will adopt the same strategy, but we have made this decision in Western Australia to start it off and to go alone, and we hope that others will follow."

Teenagers were being targeted because they were the most susceptible and the biggest carriers of the meningococcal bacteria, Mr Day said.

More than 150,000 WA students and young adults are expected to be vaccinated over the three-year program.

The cost to the WA government for the first year will be $6 million, followed by $1.5 million for each of the next two years.

Immunisations will be provided in schools and community health clinics.

A vaccination program was implemented in Kalgoorlie in December after five cases of meningococcal W in the area over a two-month period.

That program has so far administered more than 3400 vaccinations.

Mr Day also warned that vigilance continued to be vital in countering the impact of the disease in WA.