The teacher, identified as Patricia Cummings, taught at Middle School 118 in the Tremont section of the Bronx.
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Students said Cummings, who is white, singled out black students and told them to lie face-down on the floor during class.
At one point during the exercise, she stepped on the back of at least one of the students and allegedly said, "How does it feel? See how it feels to be a slave."
She was trying to teach seventh graders about the Middle Passage, the torturous journey of Africans brought to America by ship to be slaves.
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Cummings was initially removed from the classroom for a few days after the incident, returning to teach on Thursday. But after the New York Daily News called the district about the lesson, Cummings was reassigned away from students.
In a statement, the school district said, "While the investigation has not been completed, these are deeply disturbing allegations, and the alleged behavior has no place in our schools or in society."
The school system is bringing in extra counselors and the principal is meeting with students and families about what happened. Every student also will get a letter to take home.