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Announced by Associate Health Minister Jenny Salesa in South Auckland this morning, the funding targets the high rates of the illness among Māori and Pacific communities.
Rheumatic fever is an auto-immune disease that is triggered by a Strep A infection, frequently a sore throat but not always. The illness can sometimes progress to the stage where the heart is damaged.
Pacific people make up 57% of the country's rheumatic fever cases, while Māori make up 37%.
"The latest data for the 2018 calendar year suggests the rates of rheumatic fever in Pacific people are increasing, which is a serious concern," Ms Salesa said in a statement.
This year's Budget - which the Government calls the Wellbeing Budget - will fund $12 million to support programmes to reduce the illness among Māori and Pacific communities.
"We've focused this initiative on the Auckland region because two-thirds of rheumatic fever cases occur there, mainly in South Auckland.
"Targeted and tailored initiatives are shown to be more effective for improving Māori and Pacific health outcomes and we are doing more to support this approach."
Ms Salesa said the initiatives could include free school-based health clinics in disadvantaged communities.
"To have the greatest chance of success, it is crucial that initiatives and solutions are community-led and whānau-driven.
"The Ministry of Health will work closely with the Auckland region district health boards and key Māori and Pacific providers to achieve this."