A five-year-old girl thought to have bird flu died at the Sulianti Saroso Hospital in North Jakarta on Wednesday morning, Minister of Health Fadilah Supari said.
"It's most likely she died of the bird flu," Siti said, adding the tests were still being carried out to determine the cause of the death.
The girl, identified as RIS, was a resident of North Jakarta.
The minister said that the girl was admitted to Sulianti Saroso Hospital on Tuesday after being treated for five days at a hospital in Central Jakarta.
The government said on Tuesday that six people had been hospitalized with symptoms of avian flu, including an employee and a vendor at Jakarta's Ragunan Zoo. It declared the outbreak and " extraordinary" situation.
Officials decided to close the zoo on Monday for the next three weeks after some 19 birds tested positive for the virus.
The government confirmed last week that the 37-year-old Rini Dina, who lived near a chicken slaughterhouse in a South Jakarta suburb, was the fourth human fatality linked to bird flu in the country.
In July, Indonesia became the fourth country in Asia to record human cases of the disease when a man and his two daughters died after contracting bird flu.