Nine high schools in three buildings that were evacuation shelters after Hurricane Sandy will remain closed to students on Wednesday, the city Department of Education said late Tuesday.

Franklin Delano Roosevelt High School in Brooklyn still has about 800 shelter residents and will remain closed, the D.O.E. said. George Washington Educational Campus in Washington Heights also still has shelter residents and would remain closed Wednesday, too, the agency said.

The third campus that will stay closed on Wednesday is John Jay Educational Campus in Park Slope, Brooklyn, where about a dozen evacuees came down with the stomach flu. The school, which houses four schools, will be cleaned and likely would reopen on Thursday, the agency said.

The D.O.E. also hoped to open schools in two other buildings, F.D.R. and George Washington, by Thursday. The information about school openings remained in flux Tuesday evening.

Four high schools will continue to serve as hurricane shelters even though students will return to classes there on Wednesday. According to the D.O.E., about 250 shelter residents will be housed on the seventh floor of Brooklyn Technical High School while the school opens its doors to students. Hillcrest High School in Queens will open for classes while approximately 200 shelter residents will remain in its gymnasium, the agency said.

On Staten Island, Susan Wagner High School will open with about 150 shelter residents still living in the gym. Tottenville High School will reopen to students and will stay open during the night for residents who do not have heat and need shelter, the D.O.E. said.

The High School for Graphic Communication Arts on West 49th Street in Manhattan would reopen after all shelter residents were moved out, the D.O.E. said.

Earlier on Tuesday at that school, volunteers stacked folded cots in the outside entrance area and piled up garbage bags containing the belongings of the temporary residents as that shelter was shut down ahead of the students’ return on Wednesday

The residents, who included people displaced from homeless shelters around the city because of the storm, milled downstairs waiting for yellow school buses to take them to another location. Many were confused about what was happening, but had no options but to go where there was shelter.

“It’s been tragedy on top of tragedy,” said Anthony Jones, who had arrived at Graphic Communication just that morning looking for a place to stay with his wife, 9-year-old son and 17-year-old daughter. They had been displaced from the Henry Street Settlement shelter for homeless families on the Lower East Side during the storm and had been staying with friends until Tuesday.

“We had to go because another family with five people came in and there were 17 people in a two-bedroom apartment,” Jones said. He said they would take the bus from the midtown school to the other shelter, which Red Cross volunteers said was still operating at George Washington Educational Campus, which houses four smaller high schools.

The moving of residents from school buildings came as city officials balanced the need to provide temporary housing for storm evacuees with the need to return schools to their original purpose.

During a visit to F.D.R. on Monday, a large FEMA truck was parked at the school and inside, Red Cross stations had been set up. A room in the cafeteria was full of clothing and other donations and a makeshift play area had been set up for small children who had been staying there since the storm. Evacuees said they were sleeping in second floor classrooms.

Scene outside Franklin Delano Roosevelt High School in Brooklyn, where a hurricane shelter is housed.

Among the evacuees were Eric Johnson, 26, and his wife Lina, who had walked to the school during the height of the storm after water filled their basement apartment in Coney Island. “Everything is gone, everything,” he said. “The landlord is gone. There’s nothing we can do about it.”

The couple said they were renting the apartment and had no family or friends to take them in. They were hoping to receive help from the Federal Emergency Management Agency.

Jesse Isla, a junior at F.D.R., said he was proud that his school was being used to help people in need. “Its giving homes to some people who lost it all,” he said. “That’s something to like follow as an example.”

The shelter did not stop the high school football team from practicing on Monday. Football coach Paul Klyap said the practice was called to try to bring some normalcy to kids who like many others have been going stir crazy since the storm.

“This is more just getting them together, a little diversion if nothing else.” Klyap said there were about 10 kids missing from practice and two who haven’t been heard from yet.

“It’s a bad situation inside,” said Klyap. “There are people that are just struggling. We’ll try to do our best. We’ll try to keep these guys busy and safe.”