Howard encountered the woman on a visit to Colac, an outback town with 500 people in the southern state of Victoria.
Supporters turned up to greet the prime minister along with angry Aboriginal protesters and the woman, known only as Moopor.
Painted in traditional tribal makeup and wearing possum skins, Moopor stood silently and cast the curse by pointing a small bone at Howard as he climbed into a waiting car. Howard smiled and waved at Moopor before leaving.
Moopor refused to speak with reporters, citing unspecified Aboriginal cultural reasons.
It was not clear what effect the curse was intended to have on the prime minister.
Geoff Clark, the chairman of the soon-to-be scrapped Aboriginal and Torres Strait Islander Commission, said the curse was a warning for Howard.
"Mr. Howard can ... ignore the message at his own peril and be put under a curse up until the next federal election," Clark told reporters.