The announcement has been made as Mr Downer launched a policy for development assistance in health.
"We want to do more than we have been doing to address the malaria problem," he said.
"Solomon Islands and Vanuatu are two very good places to focus on.
"Since there are solutions to the problem of malaria, we need to work at them.
"Obviously to solve the whole problem would be simply a massive task but to start implementing programs there I think will be very useful."
The initiative for Solomon Islands and Vanuatu will start with a research and mapping exercise to identify and target islands and provinces.
The aid bureau, AusAID, says priorities in fighting malaria are disease surveillance and control, buying supplies and delivering basic services.