Education department officials may be compelled to answer questions about the beleaguered system for tracking students with disabilities, a Manhattan Supreme Court judge ruled Thursday.

The decision comes as the result of a lawsuit filed in February by Public Advocate Letitia James, which claimed that flaws in the city’s system has resulted in missing support services for students and the loss of millions of dollars.

Known as the Special Education Student Information System, or SESIS, the $130 million system was designed to keep track of the over 200,000 students who receive special education services, and make sure that they actually receive the supports outlined in their individual learning plans.

But SESIS was criticized almost as soon as it launched in 2011. Teachers said it was glitchy and, in some cases, virtually non-functional — and even the city has acknowledged that the data it produces is unreliable. James’ suit also claims SESIS’ problems contributed to the loss of $356 million in Medicaid money.

Judge Lynn Kotler’s decision grants a “summary judicial inquiry,” a rare proceeding that compels city officials to publicly answer a judge’s questions about the tracking system, according to the Public Advocate’s office.

In the decision, Kotler wrote that the inquiry is warranted partly because “the underlying facts have not yet been fully disclosed to the public and/or are otherwise not undisputed.”

It is not entirely clear exactly how the inquiry will unfold; in fact, the judge noted that this particular legal proceeding hasn’t occurred since 1900.

For its part, an education department spokesperson wrote in an email that the city is “reviewing our options” but would not elaborate further about a potential appeal.

James celebrated the ruling as a step forward. “This dysfunctional system has not only let down our children with disabilities, but has also cheated our taxpayers,” James said in a statement. “This is an important milestone towards justice for every child and family that has suffered at the inadequacy of the Department of Education.”

Both sides are scheduled to meet Sept. 20 to set a hearing date.