New York City schools had the most “violent and disruptive incidents” in the state last year — accounting for more than half, with incidents including assaults, sexual offenses and bomb threats, a new report reveals.

The data released Tuesday by state Comptroller Tom DiNapoli shows 17,991 incidents out of 32,084 statewide came from Big Apple public and charter schools — or 56% of the state’s total.

That’s out of 1,817 city schools, which serve 1.1 million pupils — 40% of the state’s 2.7 million students.

“In order to learn effectively, students need to feel safe. Sadly, many students and faculty are confronted with violent and disruptive activity on a regular basis,” DiNapoli said.

The shocking data comes a day after The Post revealed more than 1,600 knives were confiscated in city schools last year, the highest figure in at least five years and up drastically from the 873 blades seized in 2015.

DiNapoli’s study shows New York City schools logged the highest overall incident rates last year — coming in at 16.9 incidents per 1,000 pupils, followed by the Capital District showing 12 occurrences per 1,000 kids.

Schools break down disturbances into categories including homicides, assaults, weapons possessions, sexual offenses and bomb threats.

The city led the state in sexual offenses — recording 3.3 per 1,000 students. That’s three times higher than the second-highest region, the Mohawk Valley, with 1.1 per 1,000.

The city also had a high assault rate, at 8.3 assaults per 1,000 students, and

However, the five boroughs did have the lowest alcohol- and drug-related incidents in the state, cataloging 1.9 reports per 1,000 pupils.

One-fourth of all public and charter schools, about 1,210 institutions, across the state claimed they experienced not one single incident.

But only 8.3% of city schools reported zero incidents — compared to 47.2% from Long Island.