The parents were joined by elected officials and say the school's Chancellor went too far.
The latest chapter in the book of issues over shared space in public schools, involves the building shared by the Girls Prep Charter School and a school for autistic students, known as P.S. 94.
Girls Prep this year will expand to include middle school grades, in space now used by the autism program.
The state education commissioner ruled that the city did not follow all the procedures for allowing public input on its plans for girls Prep. But state law allows schools chancellor Joel Klein to take emergency action, which he did, over strong words of protests.
The city has issued a statement which says: "Not a single autistic child in this program would be moved from their current location under our proposal. The emergency declaration would solely be to provide space for 84 middle school girls who start school in one week and, without our immediate action, would not have a place to learn."