New York City yeshivas collect more than $100 million a year in taxpayer funds — a lot to lose if the religious schools are found to deny students basic instruction in English, math and science.

State Education Commissioner MaryEllen Elia released new guidelines in November that give her the power to yank funding from yeshivas and other private institutions that fail to provide a “substantially equivalent” education to public schools.

Much is at stake. The city Department of Education gave Jewish day schools $97 million for teachers, books and afternoon busing last fiscal year, the DOE told The Post. But that’s only a partial accounting of the largesse, officials acknowledged.

The yeshivas — like other non-public schools — get millions more for pre-K programs, special-ed, food, child-care, security, technology and record-keeping on immunizations, attendance and state exams.

“If you add all the state and federal funding, it would be at least twice as much,” said Naftuli Moster, the founder of YAFFED, a group seeking enforcement of state standards. It spurred a probe, which has dragged on for 3 ¹/₂ years, of 39 yeshivas accused of skimping on secular education.

The DOE has yet to comply with The Post’s Freedom of Information Law request for funding data on the 39 schools — a request filed 22 months ago.

Four Brooklyn yeshivas, all high schools, have refused to let DOE inspectors inside to review their curricula, Chancellor Richard Carranza has told the state.

“For those yeshivas that refuse inspection, their funding should be shut out of any DOE contract,” said Patrick Sullivan, a former member of the city’s Panel for Educational Policy, which approves school contracts.

Avi Greenstein, leader of a group formed to defend the yeshivas, has said the schools want clarification on the state guidelines. Greenstein did not return messages last week.

Of $84 million in federal aid for academic instruction in non-public schools with low-income kids last year, the DOE funneled $36 million to 103 yeshivas, said DOE spokesman Will Mantell.

The DOE also distributed $7 million in state funds to 201 Jewish schools for books, and $54 million in state and city cash to 133 yeshivas for busing after 4 p.m., Mantell said. He did not give a figure for busing earlier in the day or list all funding for other services.

Some ultra-Orthodox parents have transferred their kids to more progressive yeshivas to give them a better secular education, or they pay for extra tutoring.

“I don’t care about the taxpayers,” one mom told The Post. “I care about having to pay $300 for a math class my 12-year-old son has to take at 6 to 7 p.m. after a long day of Jewish studies.”

Meanwhile, some yeshivas have been accused of ripping off taxpayer funds or have come under FBI investigation. Last March, two former staffers of the Williamsburg-based Central United Talmudical Academy pleaded guilty in Brooklyn federal court to stealing $3.2 million that the state Health Department paid to feed needy kids.

Overall, the city spends at least $255 million a year for non-public schools, including $151 million for transportation, according to Doug Turetsky, a spokesman for the Independent Budget Office.

Additional reporting by Doree Lewak