Cecile Manorohanta said in a statement she resigned in the wake of the demonstrators' deaths Saturday, the German broadcaster Deutsche Welle reported Monday.
Witnesses said at least 28 people were killed and 200 others wounded after police fired on demonstrators who were marching toward the presidential palace in the Madagascar capital of Antananarivo.
The shootings came after an estimated 20,000 people gathered in the city for a rally in support of opposition leader Andry Rajoelina, who is challenging President Marc Ravalomanana, Deutsche Welle said.
Haile Menkerios, U.N. assistant secretary-general for political affairs, expressed concern about events in Madagascar after meeting Ravalomanana on Monday. Menkerios said he and U.N. Secretary-General Ban Ki-moon felt "extreme sadness" over the shootings and were calling for those responsible from both sides to be arrested, the BBC reported.