About 5000 South Australian children aged under five who have pre-existing health issues are now eligible to receive a COVID-19 vaccine.

The doses are being rolled out from Monday under new national guidelines.

Eligible children are those severely immunocompromised, have a disability, or have complex or multiple health conditions that increase the risk of severe illness from the coronavirus.

They include cancer patients or those on immunosuppressive treatments, children with complex congenital heart disease, chronic lung disease, type 1 diabetes and those with a disability such as cerebral palsy or Down syndrome.

They will be given a lower pediatric dose of the Moderna vaccine which is a quarter of the adult dose.

"Expanding the COVID-19 vaccine rollout will help protect our most vulnerable babies and children from becoming severely ill and ending up in hospital," Health Minister Chris Picton said.

Families can access the jabs at Adelaide's Women's and Children's Hospital, selected regional SA Health clinics, participating GPs, Commonwealth vaccination clinics, and through Aboriginal Community Controlled Health Organisations.

SA Health will also set up a vaccination clinic on Kangaroo Island this week for the newly eligible age group, operating on Thursday and Friday, while mobile clinics will roll out across regional areas later this month.

Two doses are recommended, with an eight-week interval between each dose.

However, severely immunocompromised children are required to have three doses.

The program follows approval by the Therapeutic Goods Administration and the Australian Technical Advisory Group on Immunisation.