New York’s charter school bigwigs are “deeply troubled” by state education officials who they claim are stunting the growth of the publicly funded alternative schools — instead of embracing its success in the classroom.

Fourteen charter leaders sent a scathing letter to state education boss Betty Rosa on Monday, slamming her department and the Board of Regents for allegedly undermining the schools approved by the State University of New York.

“Unfortunately, SUNY’s success has made it a target,” the letter fumed.

“Teachers unions and other opponents of charter schools cannot credibly argue with the results being produced by SUNY-authorized schools, particularly for students in underserved communities.”

Both SUNY and the Board of Regents — the policy board which oversees the state’s education department — have the authority to approve charter schools.

But thanks to a bureaucratic quirk in the law, the Board of Regents reviews applications approved by the more charter-friendly SUNY Board of Trustees/Charter Schools Institute — and often opposes them.

The performance gap between SUNY-authorized schools and Regents-authorized charter schools was a whopping 17 percentage points in English Language Arts and 21 percentage points in mathematics in recent years, Success Academy Charters Schools CEO Eva Moskowitz and Zeta Charter School Schools CEO Emily Kim said.

“New York’s education officials should not be fighting success,” the letter said. “New York’s students need more of what is working, not less.”

The charter school leaders said they’re “deeply troubled” by “repeatedly second-guessing” SUNY’s decision-making and “even supporting” lawsuits challenging SUNY-authorized schools, which serve more than 117,000 students across the Empire State.

“Instead, they have increasingly sought to attack the institution itself,” the letter added.

An SED spokesperson slammed the letter, insisting education officials are merely upholding the law.

“While the signatories to the letter boast of their strong academic outcomes, this record is not shared equally among them,” said spokesperson JP O’Hare.

“And, in any event, academic achievement does not excuse, for example, violating the New York City charter cap or ignoring community opposition to new schools.”

Joseph Belluck, chairman of the SUNY Charter School Committee, argued SED and the Regents have gotten more aggressive against charter schools.

“They oppose every little thing that has to do with charter schools,” he said, adding that SUNY is abiding by the charter school cap.

Although several bills have been floated in Albany to strip SUNY of its power to authorize charter schools over the last few years, none have passed.

Meanwhile, a source told The Post some of the charter school administrators who signed the letter have had issues that SED flagged.

Al Cockfield of Lamad Academy has a prior federal felony conviction related to drug conspiracy and distribution, and was denied a charter application by SED, but was approved through SUNY.

The United Federation of Teachers and its state affiliate, New York State United Teachers, recently sued SUNY for allegedly overriding the state charter school cap — permitting Success Academy to transfer a charter from one of its Bronx Success Academies to a new entity, Strive Charter School, founded by Eric Grannis, the husband of Moskowitz.