Hariadi Wibisono told Reuters the results on the 25-year-old woman, who died earlier this week, made her Indonesia's eighth confirmed death from the H5N1 strain of bird flu.
"We got the result this morning. She was positive," said Wibisono, who heads a department charged with eradicating animal-borne diseases.
Officials have previously said the woman had contact with dead chickens before being admitted to a Jakarta hospital.
Another five people have been confirmed to have contracted the virus in Indonesia but have survived.
The highly pathogenic H5N1 strain is endemic in poultry in parts of Asia, where it has killed more than 60 people.
Experts fear H5N1 could mutate into a form that passes easily among people, just like human influenza. If it does, millions could die because they would have no immunity.
Most human bird flu cases in Asia have been blamed on direct or indirect contact with infected chickens.