Foreign Minister Penny Wong unveiled the multi-million dollar package as part of World Malaria Day on Thursday, with the funding going towards treatment of the disease as well as testing tools.
The government has provided $17 million for the development of new malaria treatment options that will include medicines suitable during pregnancy and for children, through a partnership with the Medicines for Malaria Venture organisation.
A further $5 million will be allocated to James Cook University to step up efforts in monitoring mosquito-borne diseases in Pacific countries, which also include dengue fever and zika.
The remaining $8 million will go towards developing malaria diagnostic tests for countries in the region, in a partnership with health organisation PATH.
Malaria remains among the leading causes of death of children under the age of five worldwide, according to the World Health Organisation.
"Malaria is not only a threat to the health and wellbeing of communities in the Pacific and Southeast Asia, it also impacts education, tourism and economic growth," Senator Wong said.
"Investing in our partnerships with our region and its capacity to test and treat malaria is clearly in Australia's interest."
Figures have shown there were more than seven million malaria cases reported in the region in 2022.
Pacific Minister Pat Conroy said Australia aimed to provide critical support to countries battling with malaria outbreaks.
"We are investing to support our region with better surveillance, better control to prevent infections, better diagnostics to detect cases and better medicines so people with malaria receive the best possible care," he said.
