Officials recorded 20 cases of the illness last year, 19 of them fatal, the Health Ministry said in a statement.
The figures are the first to be released by Indonesia since March, when four deaths were announced. They show that while avian influenza is still active, the number of cases is on the decline.
Last year saw the lowest number of human fatalities since 2005, when 13 were reported.
The ministry said that the most recent death was on Sept. 23, but gave no details about who had died or where.
Bird flu has killed 282 people worldwide since it began ravaging poultry stocks in 2003, the WHO said on its Web site. Indonesia is the worst affected country, with 161 infections since 2005, 134 of them fatal.
Indonesia came under strong criticism last year when it stopped announcing individual cases of the disease and ceased sharing virus samples with international health experts working on a vaccine.
Indonesia's former health minister had argued that the global system for a vaccine was unfair because her country's bird flu specimens could be used for a cure that would ultimately be too expensive for most Indonesians.
