Children with a disability born in Australia to parents on temporary visas will get access to help in South Australia under an $11 million program.

The funding, over five years, will provide practical and therapeutic support, including the provision of ability aids, to children who need special care, assistance and treatment.

Premier Peter Malinauskas says these children are not eligible for help through the National Disability Insurance Scheme.

"We can afford this. We can choose to prioritise this," the premier said on Thursday.

"It is wrong that young people born in this country to parents who love this country and contribute to it and who are born with a disability are left behind."

Human Services Minister Nat Cook said she had raised the issue with the federal government of such children falling through cracks in the NDIS and would continue to do so.

"It's a conversation that will remain active," she said.

Only a small number of children are expected to draw on the funds each year, with five receiving help in SA.