The District’s public charter schools discriminate against students with disabilities — especially those with significant needs — in their admissions policies and often steer them instead to expensive private schools, special education advocates contend in a complaint filed Thursday with the Justice Department.

The city’s 52 publicly financed, independently operated charter schools, which educate nearly 29,000 students, are supposed to be open to all, with admission by lottery when demand exceeds available slots. But attorneys for the Bazelon Center, a nonprofit legal advocacy group, cite data showing that the city’s traditional public schools serve far more students with the highest level of needs than the charter schools do.

“The District’s charter school system is not open on an equal basis to all students,” Bazelon legal director Ira A. Burnim wrote in the complaint, filed with the department’s civil rights division. He added that the charter system “contributes to and aggravates the longstanding failure” of all D.C. schools to properly serve the city’s most vulnerable and fragile children.

Leaders of two charter schools named in the complaint denied discrimination.

Brian Jones, chairman of the D.C. Public Charter School Board, which oversees the charter sector, said the issue was difficult to analyze because most charters act as the legal equivalent of a mini-school district. They are answerable to D.C. and federal agencies on special education issues.

“I wouldn’t say any of the public schools in the District [regular or charter] are where we would like them to be,” Jones said. “But I am not in a position to say we have a systematic problem in the charter schools.”

The complaint places the District at the leading edge of an emerging national debate over whether the charter school movement — born with the objective of providing more public education options — is adequately serving students with special needs.

Last month, a federal judge refused to dismiss a lawsuit against the Louisiana Department of Education brought by the Southern Poverty Law Center on behalf of thousands of New Orleans special education students. The lawsuit alleges that students are denied access to the city’s charter schools.

“I think that what’s going on in D.C. does track with what we are observing nationwide,” said Brenda Shum, senior counsel for the Lawyers’ Committee for Civil Rights Under Law, also a party to the New Orleans case. “There’s an ongoing concern that charter schools are not necessarily equipped to implement their obligations.”

The Justice Department could decide to start an investigation of the charter schools or seek to negotiate an agreement. It could also file a lawsuit.

Bazelon’s complaint does not cite specific instances of discrimination. But it draws together anecdotal and statistical evidence suggesting that children with disabilities are underrepresented in D.C. charter schools. According to District officials, 18 percent of the city’s traditional public school population receive special education services. That figure includes more than 2,000 students in private schools at public expense because it was decided that their needs could not be met in the city system. Eleven percent of the charter population is made up of special education students.

The disparity becomes more clear in the case of children with the most complex emotional and physical needs. The document cites a 2010 report by federal court monitors overseeing the city’s special education system that shows that city public schools serve three times as many of those students (1,551) as charter schools do (560). Charter students with especially significant needs tend to be concentrated in three schools: St. Coletta, Options and Sail.

According to the complaint, some charter schools include questions on admission applications asking whether a child has received special education services.

The complaint alleges that several charter schools openly discourage parents of special education students from enrolling. Parents have lodged grievances with the District about the Cesar Chavez Public Charter School and William E. Doar Jr. Public Charter School. The parents said the schools told them that they cannot serve children with significant special education needs.

Maia McKinney, Doar’s interim executive director, said Thursday that she strongly doubts any parent received such a message. “We have practiced non-discrimination,” she said. “Any and all students with special needs are welcome. We are a public school.” About 13 percent of Doar’s 530 students have special education status.

Jeff Cooper, managing director and chief operating officer for the three Chavez campuses, where about 12 percent of the 1,285 students receive special education, also denied allegations of discrimination.

Lakita McNeil, whose 13-year-old son Jared was expelled this year from Chavez’s Bruce Prep campus, said in an interview Thursday that her son was unfairly treated.

McNeil said Jared did not enter the school with special education status but later received a diagnosis of “oppositional defiant disorder,” a behavior issue requiring him to spend five hours a week outside the classroom receiving special services.

McNeil said she was told by school counselors that “you might want to start looking for other schools.”

She said Jared, who now attends Deal Middle School, was eventually expelled for behavior issues that school officials say were not related to his disability. McNeil contends that he was forced out because he was disabled.

Cooper said the contention was “absolutely false.”