South Australian health authorities says the take-up of a free vaccination program for B strain meningococcal disease has been disappointing.

Up to one-third of South Australia's children and young adults are missing out on protection from the deadly B strain meningococcal disease, health authorities say.

Communicable disease control director Louise Flood says the uptake of a free vaccine program has been disappointing.

So far only about 70 per cent of the required number of doses to protect children up to the age of four and young adults aged 17 to 21 have been distributed.

"South Australia is the first state in Australia to offer free vaccination against the potentially deadly meningococcal B disease, and we are urging parents and eligible young adults to talk to their GP or immunisation provider to have their children or themselves vaccinated," Dr Flood said.

"Winter and spring are typically the time that we see more cases of meningococcal disease, so now is the perfect time to take advantage of the free program and get vaccinated."

Before the free program, it cost parents up to $500 for a full vaccination course for the B strain, the most common form of meningococcal disease in SA.