Maritza Tamayo, head of the Unity Centre for Urban Technologies, hired Gilda Fonte to carry out a series of Santeria ceremonies. Santeria blends traditional African religions and practises, such as animal sacrifice, with Catholicism, and was first practised by slaves in the Caribbean.
Ms Tamayo was accused of asking Ms Fonte to lead a ceremony in which chicken blood was used to cleanse the school's buildings of negative energy.
In another ritual, Ms Fonte balanced a silver tray with 40 lit candles on her head.
Melody Crooks-Simpson, the school's former assistant principal, said she had been forced to attend a ceremony at which all the women wore white dresses and that she had been made to pay $900 (pound;443) to participate.
Richard Condon, New York's special commissioner of investigation for schools, said the reason for dismissing Ms Tamayo had nothing to do with the type of religion involved, but was because she had made staff participate. "Had she hired a priest to sprinkle holy water on the building and she coerced the assistant principal into paying for it and attending it, I would still have a problem with it," he said.