Public Advocate Letitia James has filed a lawsuit against the city education department, alleging that flaws with its special-education data system have resulted in missing support services for some students and the loss of millions of dollars.

The lawsuit centers on the embattled $130 million Special Education Student Information System, or SESIS. That system was designed to allow educators to more easily keep track of the learning plans created for each of the city’s more than 200,000 students with disabilities, and to make sure the students receive their mandated services.

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However, the system came under fire almost immediately after it was rolled out in 2011. Teachers reported that it was glitchy and burdensome, and the city comptroller blamed the system for keeping the city collecting millions of dollars in federal Medicaid reimbursements for low-income students with disabilities.

Now, James is taking those longstanding critiques of the Bloomberg-era system one step further by filing the lawsuit, which claims that problems with SESIS contributed to the city losing out on $356 million in Medicaid dollars over several years.

“The program doesn’t work and it never has,” James said at a press conference Monday. “The failure of the system has been one of the department’s worst-kept secrets.”

When former City Comptroller John Liu made a similar claim in 2013, city officials denied that Medicaid reimbursements are in any way affected by SESIS. On Monday, a city law department spokesman said the city plans to review James’ lawsuit.

The latest attack on SESIS comes on the heels of a U.S. Department of Justice investigation that found the city provides “inexcusable” accommodations for its young students with disabilities and has failed to address the problem for years. On Friday, the city formally rejected the findings that two-year investigation by the office of Manhattan U.S. Attorney Preet Bharara, the New York Times reported.

School staff working with special-education students are required to log information into SESIS about each student’s “Individualized Education Program,” or IEP, including details about initial evaluations, meetings with parents, services provided, and any changes made to the plan. But the system suffered from so many technical problems early on that teachers had to input data on evenings and weekends, which eventually led an arbitrator to order the city to pay $38 million in overtime to more than 30,000 educators.

Advocates have other complaints. Ellen McHugh, a longtime special education advocate and James’s appointee on the citywide council on special education, said parents should be able to access the system to keep tabs on their children’s progress.

“We can’t, as parents, access our child’s IEP,” she said. “We can’t, as parents, find out that our IEPs are being implemented.”

Maggie Moroff, special education policy coordinator for Advocates for Children, said that many students with disabilities do go without their mandated services. While she hesitated to lay the blame completely on SESIS, she said the city needs to make sure that no students fall through the cracks.

“There are lots of kids going on without their services,” she said, “and there doesn’t seem to be a system designed to flag that.”

The public advocate’s office has set its sights on the city’s handling of students with disabilities before. In August, James joined a lawsuit — which is set to start oral arguments in April — that claims the city is violating a local law that requires students with disabilities to be transported in air-conditioned buses when it’s particularly warm outside.

“We go wherever the facts lead us,” James said, “and, unfortunately, a significant number of complaints that we have received are from parents with special needs children.”

An education department spokesman did not comment directly on the lawsuit’s claims about SESIS.

However, he said that more school staffers had been trained to use the system. He also noted that the city has taken other steps to boost its supports for students with special needs, including launching more programs for students with autism and hiring 300 additional occupational therapists.