City investigators are accusing a Manhattan charter school that focuses on serving special education students of violently disciplining students and covering up the abuses.

Staff at Opportunity Charter School allegedly punched one student, threw another to the ground and pulled a third out of a classroom by her hair during the 2007-08 school year, according to a report released today by the city’s Special Commissioner for Investigation. The report documents a total of six cases of verbal and physical abuse.

According to the report, the school’s staff members who were accused of violently disciplining students were never punished themselves. The accused staff include the school’s administrative director, a dean of students, and specialists trained to work with special needs students. In some cases, the school also failed to document cases of physical and verbal abuse in its own incident reports.

“The staff conduct at OCS during the 2007-2008 school year went beyond restraint and could be considered condoned assaults and abuse of schoolchildren,” the report concludes.

In a statement sent to reporters, a representative of the school said that Opportunity investigated the cases during the school year the abuses allegedly happened and has since improved its discipline and reporting practices.

“Opportunity categorically disagrees with the report’s assertion that the oversight and reporting lapses that occurred two years ago ‘could be considered condoned assaults and abuse of schoolchildren,’” the statement said. “There is nothing in the Commissioner’s report that substantiates that accusation.”

A year after the alleged abuses, Opportunity hired a new principal. The two school leaders accused of covering up the abuses still work at the school. One, Betty Marsella, is now the Director of External Development and works at home. The other, Leonard Goldberg, is now the school’s chief executive officer.

City officials, who authorized the charter school and forwarded investigators the anonymous tip about abuses that launched the inquiry in June 2008, said the school has cleaned up its act since then.

“The school has been extremely responsive to the charges from two years ago,” said city Department of Education spokesman Jack Zarin-Rosenfeld. “They have made changes in senior administrators, implemented strong new oversight policies, and created a Human Rights Committee that reviews all incidents involving students.”

The city initially recommended a two-year probationary period for Opportunity in late 2008. In its second report six months later, the DOE downgraded its endorsement to a one-year period, considering how the school was adjusting its disciplinary practices in that decision, Zarin-Rosenfeld said.

In February, the city endorsed a three-year renewal of Opportunity’s charter, and the state Board of Regents was scheduled to vote on the city’s recommendation this month. The city asked the Regents to postpone their vote until next month to give the board time to review the SCI report before voting, Zarin-Rosenfeld said.

The combined middle and high school, which opened in 2004, has followed a rocky path from its start. Roughly half of its students receive special education services, and the school has struggled to boost its students to the level of progress the city expects.

Here’s the full report issued by the Special Commissioner of Investigation: