Siti Fadilah Supari said the 15-year-old girl, who died in hospital in the Central Java city of Semarang on November 7, was not carrying the H5N1 strain.
"Both tests came back negative," she said.
The girl, who lived near a chicken slaughter house, died 10 days after complaining of flu-like symptoms.
Indonesia has been the country hardest hit by bird flu, with its official toll of 112 deaths accounting for nearly half of worldwide deaths from the disease.
The H5N1 virus typically spreads from bird to human through direct contact, but experts fear it could mutate into a form easily transmissible between humans, with the potential to slaughter millions in a pandemic.