Leaders of independent, Catholic and Jewish schools reacted with elation to expanded funding for nonpublic schools for the 2016-17 academic year included in the just-passed state budget.

“Not only does this funding help thousands of kids whose schools like ours face funding challenges, it also should be seen as a step toward breaking down the walls that have prevented public, private and parochial schools from working together to help all of our kids,” Joshua Crane, head of school at The Stony Brook School, said Friday.

“Contrary to popular belief, many private schools are not flush with financial resources, and therefore additional revenues outside of tuition and fundraising can and will provide a needed lift,” Crane said. The independent preparatory school in Stony Brook, founded in 1922, has 360 students in seventh through 12th grade.

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The state funding includes $2 million for a new Office of Religious and Independent Schools to serve the state’s nonpublic and religious schools.

The State Senate and Assembly, along with Gov. Andrew M. Cuomo, also increased security grants to nonpublic schools from $4.5 million to $15 million, said Morris Peters, a spokesman for Cuomo. The money, to be applied over the next two years, will help pay for private security guards, along with training and health and safety equipment.

The Comprehensive Attendance Policy program, or CAP, which provides nonpublic schools with reimbursements for tracking and enforcing student attendance, will be accelerated to reduce the reimbursement lag from two years to one year, Peters said. The total amount to be paid out will be increased to $60 million.

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Officials also agreed to have the government pay out the second half of a $250 million, two-year appropriation enacted last year for mandated services in nonpublic schools.

Some school leaders saw the increases as a breakthrough in government efforts to assist private schools, which they said save taxpayers millions of dollars.

“It is exceedingly helpful when the state of New York and Catholic schools cooperate together,” said Brother Gary Cregan, principal of St. Anthony’s High School in South Huntington. “Saint Anthony’s High School saves the taxpayer $35 million a year by privately educating students, so it is appropriate that the state supports us in this great mission of educating our country’s future.”

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St. Anthony’s, with 2,275 students, is one of 10 Catholic high schools on Long Island, and is among those that have seen enrollment increase in recent years, even as declining numbers of students in Catholic elementary schools have forced closures.

Cindy Dolgin, head of school of the Schechter School of Long Island, with campuses in Williston Park and Jericho, said she was “thrilled that through this legislation, our state government has appropriately recognized that there are basic needs of students within all schools in New York, whether public or private.”

Schechter’s Lower School, with kindergarten through fifth grade, is in Jericho, and the Middle and Upper schools that serve seventh- through 12th-graders are in Williston Park.

Security costs “have skyrocketed over the past few years, ever since the massacre at Sandy Hook Elementary School in Connecticut,” she added. “All schools need to be safer for the benefit of all state residents, both children and adults. Students cannot properly learn in school if they do not feel safe.”

Leaders of the Orthodox Union, a Manhattan-based educational and social service organization that serves the North American Jewish community, said they want to see the new state office help strengthen instruction in science, technology, engineering and math — STEM programs — in nonpublic schools.

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The Stony Brook School’s Crane said he hopes the impact of the legislation will go beyond funding issues, serving a greater goal to “help to begin breaking down the barriers between private, parochial and public schools. For too long we have been sealed off from each other, missing out on vital interchange regarding curriculum, pedagogy and best practices.”