The latest death, announced on Wednesday, was a 15-year-old boy whose preliminary tests were positive for the H5N1 virus.
It comes as international health officials express growing frustration that they must fight Indonesia's stifling bureaucracy as well as the disease.
Indonesia, a massive archipelago of 17,000 islands that is home to 220 million people, has a patchwork of local, regional and national bureaucracies that often send mixed messages, officials said.
Indonesian health ministry officials will often meet with outside experts to formulate plans to fight bird flu, but the schemes are rarely realised, said Steven Bjorge, a World Health Organisation epidemiologist in Jakarta.
Indonesia has logged at least 36 human deaths from bird flu in the past year - 25 since January - and is expected to soon eclipse Vietnam's 42 fatalities.
The two countries make up the bulk of the world's 127 total bird flu deaths since the virus began ripping through Asian poultry stocks in late 2003.
Attention has been fixed for the past week on one village on Sumatra island where six of seven relatives died of bird flu. An eighth family member was buried before samples were collected, but WHO considers her part of the cluster.
Experts have not been able to link contact between the relatives and infected birds, which has led them to suspect limited human-to-human transmission may have occurred. But no one outside the family of blood relatives - nor spouses - has fallen ill and experts have said the virus has not mutated in any way.
Scientists believe human-to-human transmission has occurred in a handful of other smaller family clusters, all involving blood relatives.
Experts theorise that may mean some people have a genetic susceptibility to the disease but no evidence supports that.