Parents at a Harlem elementary school are protesting the education department’s decision to place a Columbia University-affiliated public secondary school in their building starting next year.

Education officials said they chose P.S. 36 to house the Columbia Secondary School of Math, Science and Engineering because the elementary school’s population is 300 students below capacity. But some parents at P.S. 36, which serves pre-kindergarten to second grade, say the school doesn’t have room for the older students. They promised to fight back against the proposal at a meeting tonight with department and university officials.

“This is an early childhood school, this is a little people school. They’re not comfortable with sixth grade being here with their little ones,” the school’s Parent Teacher Association president, Kim Wynn, said, of the parent reaction. “They want to know why they can’t build a building somewhere else instead of taking up the space we need.”

Carmen Perez, an alumnus of P.S. 36 and a community liaison for Assemblyman Keith Wright, is organizing a petition against the new school.

“It’s insane what they’re proposing,” she said. “I saw that the parents had protested vigorously and won.”

She was referring to parent groups at two public schools who fought Bloomberg administration proposals to install charter schools in their buildings last year. Parents at the New Explorations into Science, Technology and Math School on the Lower East Side and P.S. 154 in Harlem won bitter, public campaigns to keep new schools out of their buildings, and the preliminary reaction of parents at P.S. 36 has raised the specter of a similar battle.

Currently, 600 city schools don’t have a building all to themselves, a number that has gone up under Bloomberg administration efforts to create more small schools around the city. In a letter to principals last month, the schools chancellor, Joel Klein, wrote that the number would probably continue to increase.

“It’s our obligation to use all DOE space to the benefit as many students as possible,” a Department of Education spokeswoman, Kelly Devers Franklin, said.

Tothe parents’ worry that mixing the older and younger students would be harmful to the younger ones, Ms. Devers Franklin said,”It’s actually a model researchers have found is good for kids,”she said.

The Columbia school’s principal, Jose Maldonado, is cutting a trip to Puerto Rico short to fly back for the meeting with parents.

“I’m more than willing and eager to make both schools the best they possibly can be,” he said, adding that he has already begun talking to the principal of P.S. 36 about how the two schools can work together.

The secondary school is a public school, but Columbia has promised to provide its building. The secondary school’s timetable for moving out depends on whether and how soon Columbia is able to build on the plot of land intended for the school at the corner of 125th Street and Broadway, however. The proposed spot is currently home to a McDonald’s and a part of the university’s planned expansion of its campus into Manhattanville. The expansion project has yet to be approved by the city, but Columbia has said it will build the new school building elsewhere if necessary.

In its first year at P.S. 36, the secondary school will serve a sixth grade class of 100 students and will add an additional grade each year until it reaches twelfth grade. A flyer sent to P.S.36 parents last week said the elementary school has room for 300 extra students and said the “projected time for completion of a new building is 3-6 years.”