An Australian-subsidised vaccine has been found to halve the number of children carrying a potentially fatal bacteria.

An Australian-subsidised pneumococcal vaccine in Fiji has halved the number of children carrying the potentially fatal bacteria since its national roll-out.

The Melbourne Murdoch Children's Research Institute conducted a study into the effects of Fiji putting the vaccine against Streptococcus pneumoniae - an infection - onto the national immunisation program.

Three years later, cases of the bacterium have halved in Fijian children.

"That ultimately means we will see fewer children suffering from meningitis, sepsis and pneumonia, fewer children dying and less brain damage and disability, which commonly occurs in children who survive meningitis," Associate Professor Fiona Russell said.

The bacteria is one of the most common causes of meningitis, blood poisoning and pneumonia which claims more than 650,000 child lives every year, the institute says.

Senior research officer Dr Eileen Dunn found vaccinated children were less likely to carry the disease-causing bacteria and people without the jab had "herd protection".

The Australian Department of Foreign Affairs and Trade funded the study through the Fiji Health Sector Support Program and the Bill & Melinda Gates Foundation.