"The result for the girl is positive," said I Nyoman Kandun, the ministry's director general for communicable disease control, on Saturday citing tests conducted by a Hong Kong lab accredited by the World Health Organisation (WHO)
With her death, the WHO has confirmed 34 bird flu fatalities in Indonesia, out of more than 120 worldwide since 2003, the vast majority in Asia.
The girl's 18-year-old brother, who also died on Tuesday with similar symptoms, was however not categorised as a victim of the deadly H5N1 strain of bird flu.
"So by definition he is not included but clinically he was strongly suspected to have been infected by the virus," Kandun said.
Indonesian tests had confirmed both as bird flu victims.
Indonesia has had more bird flu deaths than any other country this year. It has the world's second highest number of fatalities since 2003, after Vietnam. Nine Indonesians who were infected have survived.
Kandun denied suggestions that Indonesia had not done enough to curb the disease.