A Northwest Washington private school that has collected more than $16 million in tuition from the District over the past two years to serve special education students is under investigation for lax security, high rates of truancy and inadequate academic programs.

Officials of Rock Creek Academy said they have done their best to serve a population of emotionally and physically disabled children from kindergarten through 12th grade whose needs cannot be met by the city’s public schools. These include students with attention-deficit disorder, speech and auditory issues, cerebral palsy, depression and post-traumatic stress.

“We continue to make progress academically, socially and emotionally with our students. The data proves it. My staff is insulted by the allegations out there,” said Shawn Meade, president and chief executive of the 163-student school, which occupies six floors of a building on upper Connecticut Avenue near the University of the District of Columbia.

But District officials said they have received what they describe as an alarming stream of complaints in recent months from Rock Creek students and parents, including an allegation of sexual misconduct by a staff member involving a student older than 18. (Meade said the accusation was found to be untrue.) In November, D.C. police arrested an art teacher after he allegedly punched a student in the mouth following the school’s annual “Family Night.” The teacher was later fired.

At a D.C. Council hearing March 4, two Rock Creek students and one former student appealed to Chairman Kwame R. Brown (D-At Large) for help in addressing conditions at the school.

Seantrice Middleton, a junior, said she had been bullied and sexually harassed. On one occasion, she said, a boy forced his way into the girls bathroom and peeked over the stall at her.

“It shouldn’t be a school; it should be a mental institution,” she said. “Going to Rock Creek makes me think the whole world is bad.”

Landon Mills, a senior, said he has been learning the same course material over and over. “It feels like the school has sucked the spirit out of me,” he said.

In a letter this week to D.C. State Superintendent of Education Hosanna Mahaley, whose agency oversees private special education schools, Brown said he was “gravely concerned” about the testimony.

“It is absolutely unacceptable for any child to experience the things that were described at our hearing,” Brown wrote.

Mahaley said at a council hearing Wednesday that she could not comment in detail about the investigation but that the inquiry should be complete in about three weeks. Her office could decide to revoke the school’s state certification, effectively barring placement of students from the District, who make up Rock Creek’s entire student body. “My staff and I are very concerned,” she said.

Meade acknowledged in an interview Wednesday that the school has faced security and truancy issues. On an average day, he said, absenteeism runs 20 to 23 percent, a reflection of the challenges students face. But he also said that operations had been tightened in recent months with the addition of a security contractor. A three-person truancy team has been formed to go to the homes of students with unexcused absences.

“We’ve been doing everything we can to provide for these kids,” said Meade, the son-in-law of Rock Creek co-founder Richard Henning. His last job before coming to Rock Creek in 2004 was as a regional manager for Heavenly Hams, a food retailer.

Richard Nyankori, the District’s deputy chancellor for special education, said the student testimony was “heart-wrenching and consistent with what I’ve heard from parents and former staff of the school.” He said he would offer any Rock Creek parent or student “who’d like to consider another option to be in contact with us directly.”

But Nyankori also acknowledged at a hearing last week that he had been in contact with parents who said they’d had a positive experience at Rock Creek.

The Rock Creek inquiry is part of an effort by District officials to step up scrutiny of the 50 non-public schools in Washington and across the country that treat about 2,800 special needs children at public expense. They say the quality of the schools is uneven, and in some cases substandard. Last year, the District closed SunRise Academy in Northwest.

Under federal law, parents can sue the District for private placement if they think it cannot serve their child in a traditional public school or public charter school. If an administrative hearing officer agrees, the student is assigned to a private residential or day school.

Tuition averages about $36,000 a year, although some residential placements run as much as $125,000 annually. The city spent more than $280 million on private school tuition and transportation in fiscal 2010, a figure that officials want to reduce by building more capacity to serve special needs students in public schools.

D.C. officials said Rock Creek is one of the city’s most expensive non-residential schools, with annual tuition averaging $59,000. Meade disputed the figure but declined to offer details.

District officials have come under fire from some families, who have accused them of trying to “reintegrate” students into the public system to save money while treating the children’s needs as a secondary concern. Nyankori has denied the allegation.