Brookline Public Schools are scrambling to close a nearly $1.5 million budget gap for the fiscal year beginning in July, yet the School Committee is nevertheless setting aside $400,000 in case the city’s cost for private special education rises.

Public school systems that cannot accommodate certain special needs students internally often pay to send them to privately run schools that provide specialized instruction. Many communities set aside funds for the private school tuitions in case charges increase or a student with special needs moves to town. Lexington, for example, just learned a child requiring placement at a residential school is moving to town. The annual tuition is $297,000. Brookline last year saw its $5.9 million private school special education budget rise $43,000 due to tuition increases at the private special education schools it uses.

Children attending these schools typically need services that the local public school can’t provide, such as therapy for extreme behavioral issues, maintenance of multiple medical needs, or training in independent living for blind or deaf students. Most of the time, tuition for these “out of district” schools increases by a state-controlled rate pegged to inflation, which has ranged from .75 percent this year to as high as 3 percent in previous years.

But private special ed schools can raise their rates much higher if they go through a process called program reconstruction, which involves documenting needed changes in programs or staffing and the hike in tuition payments needed to accommodate them. Communities say a private special ed school that reconstructs its programs can raise its rates by as much as 25 to 40 percent. Annual tuitions are already steep, ranging from $27,000 to $102,000 per child for a day program and $108,000 to $297,000 for a residential program.

“It feels like a surprise, not because we don’t get notice, but because of the significance of the cost increase,” says Peter Rowe, Brookline’s deputy school superintendent for finance. Next year, he said, tuition for one student alone will increase $18,000 following a reconstruction. “We don’t have the ability to grow our revenue by that amount.”

The state Department of Education says 28 programs at 18 private schools have been granted reconstruction increases in the last five years, affecting 182 public school districts that are home to 1,075 special needs students. Another 22 programs at 17 private schools have applied for reconstruction increases for the 2011-12 school year. Four have already been approved.

James Major, executive director of the association representing private special ed schools, says the institutions seeking reconstruction increases are responding to the needs of the children they serve. He says enrollment is dropping at his member schools except for students with autism, but he adds that the students the schools do enroll tend to have more complicated needs. The schools raise money privately, but not enough to keep tuitions from rising, he says.

Major cited one residential program that has applied for a 5.7 percent increase in tuition to cover an additional three to four nurses to manage psychotropic medications and to expand to a full-year program.

Major said the state restricts private special needs schools to one reconstruction process every six years.