The plan will be funded by a 20-million-dollar European Union (EU) grant channelled through the World Health Organisation (WHO), the health ministry's disease control director Nyoman Kandun told reporters here.
Indonesia accounts for just under half of the 224 human bird flu deaths worldwide, according to WHO figures. The 100th victim died on Sunday, and the 101st fatality was recorded on Tuesday.
Kandun said Indonesia would need to meet with EU and WHO officials on a "routine basis" in order for the plan to work.
WHO's Indonesia representative Subhash Salunke said the strategy would focus on preventing new infections, better monitoring of the spread of the virus and continued scientific research.
"Prevention of new cases remains an urgent priority, while improving survival (rate) of those infected is another major priority," he said.
The prevention campaign would include ramped up efforts to improve hygiene in the country's wet markets and public awareness initiatives.
"The persistence of H5N1 in Indonesia has serious (global) consequences for health, economies and food security," Salunke said.
"Out of 33 provinces, in 31 provinces this is an endemic virus ... because it is present in such a vast area, the opportunity for virus and human being contact is immense," Salunke said.
The H5N1 virus is typically spread by direct contact between poultry and humans, but there are fears among scientists that the virus could mutate into a form easily transmissible between humans, setting off a worldwide pandemic.
The concern stems from past influenza pandemics. A pandemic in 1918, just after the end of World War I, killed 20 million people worldwide.