Eva Moskowitz’s Success Academy charter school chain is under fire from all sides for its harsh discipline policies and treatment of students with special needs.

The network, the city’s largest operator of charter schools, now faces an investigation by the institute that licenses charter schools in the state as well as a federal lawsuit filed by parents and a formal complaint lodged by parents with the federal Department of Education’s Office of Civil Rights.

State University of New York’s Charter School Institute is investigating whether one of the network’s schools in Brooklyn used its discipline policy to force out low-performing or difficult students. It launched the investigation in response to the revelation in October that the principal at Success Academy Fort Greene had compiled a “Got to Go” list of problematic students.

The institute has said it will not sign off on any new charter applications or renewals until it has received more information from Success and other charter operators about discipline and suspension policies, according to the New York Post, which broke the story about the SUNY probe.

Word of the investigation came roughly five weeks after parents of four former students at the school filed a lawsuit on Dec. 10 alleging that their special-needs children were denied services and pushed out of the school due to their disability status. All four students’ names appeared on the “Got to Go” list.

According to the complaint, the school’s rigid discipline code was enforced on students without regard to their special-needs status, and students with special needs were expected to behave exactly as other students. The complaint said Success Academy officials believe that accommodating children with special needs would be to give them “special lenience.”

The parents charge in the lawsuit that two of the four children did not receive Individualized Education Plans, as required by law.

“This approach has proven devastating to students with disabilities at Success Fort Greene, stunting their educational progress and emotional growth,” lawyers for the parents wrote in their brief. “Success Fort Greene regularly fails to provide students with disabilities accommodations they need in order to access education.”

In three cases, according to the lawsuit, Success Academy threatened to call either the police or Administration for Children’s Services to take the children from the school, while in the fourth case, a student was actually handed over to the police and taken to a hospital during a class trip.

The parents allege in the lawsuit that the school principal, Candido Brown, and other officials at the school and the network used the threat to call the police “as a means to compel parents of learning-disabled children to leave the school.”

Similar accusations have been leveled by the parents of 13 current or former special-needs students who on Jan. 20 filed a formal civil rights complaint with the federal Department of Education. According to the complaint, which cites eight Success schools in Manhattan, Brooklyn and the Bronx, the Success Academy network violated federal laws protecting individuals with disabilities when it denied accommodations to the students or, in some cases, pushed them out.

The parents accuse the network of refusing to provide the students with appropriate services and then requiring them to repeat a grade. They allege in their complaint that the school suspended the students multiple times without keeping formal records of their suspensions or providing alternative instruction or the due process required under federal law. And the parents charge that the school harassed them — including by calling 911 and having their children sent to the hospital emergency room when they didn’t pick them up immediately — until they transferred their children to a traditional public school.