An elite unit of the Junior ROTC at Francis Lewis HS in Queens has been disbanded after cadets allegedly branded a fellow member on the butt, The Post has learned.

The shocking incident involved the Raiders, a military-style athletic squad. It is one team among several in the school’s Junior Reserve Officers Training Corps, one of the biggest programs in the nation.

The alleged skin-scorching occurred during an overnight stay in April at the Hilton Garden Inn in Westampton Township, NJ, near the Fort Dix military base, city Department of Education and police officials said.

It did not come to light until the summer — after the teen victim’s parents learned about it, according to school insiders.

The Westampton Police Department and the Burlington County Prosecutor’s Office are investigating the alleged hazing.

“It’s a criminal investigation,” said Westampton Police Chief Stephen Ent.

Ent said the student’s behind was burned with “some kind of hot iron.”

The student’s outraged parents are considering bringing charges, according to three people with ties to the Fresh Meadows school.

At least two boys on the team have received a “superintendent’s suspension,” one said. The ouster, up to a year, is the highest level of student discipline in the city DOE.

In an Oct. 11 e-mail to staff, Francis Lewis principal David Marmor gave few details: “An allegation was made that during an overnight trip, last school year with the JROTC Raiders, there was inappropriate behavior by some of our students. The matter is currently under investigation by the NJ Police Department and by the NYC DOE.”

He added, “Pending the outcome of the investigations, all Raider activities have been suspended. We will not be planning, organizing or practicing for any upcoming Raider competitions.”

However the probe will not affect other JROTC activities such as drill, leadership and academic teams, Marmor said.

DOE rep Miranda Barbot called the allegations “deeply troubling,” and said “the school took disciplinary action once the allegations were reported.”

The Raiders team takes part in physical-fitness competitions against JROTC programs at other schools. Cadets wear Army fatigues and race through rope courses, climb walls, and carry canoes or other objects through woods and creeks.

Members of the close-knit group were tight-lipped.

“I’m not going to tell you anything,” said a student who was reportedly suspended. “If you want something from me, go talk to my parents. Don’t talk to me.” The student’s parents could not be reached.

Col. Albert Lahood, a DOE teacher and the program’s senior military instructor in the US Army-sponsored program, did not return messages.

Sgt. Lawrence Badia, who was supervising rifle drills on Friday, only told The Post: “It’s a serious allegation. I’m concerned.”

PTA mom Lisa Lovett said the principal told her he expects criminal charges.

“Some of the kids, I believe the victims, are bringing charges,” she said.

Teachers at the 4,500-student campus said the JROTC’s popularity has boosted Francis Lewis’ success and prestige.

“This is a great program that has been very good for our school,” a teacher, Arthur Goldstein, said. “The program does a lot of good for a lot of kids, and doesn’t push them to join the military. Kids take so much pride in this program. ROTC teens, in general, are the best-behaved kids.”

Teachers who serve as JROTC instructors are dedicated and hard-working, Goldstein said, and they would be “horrified by anything so barbaric.”

“I am absolutely sure none of them would tolerate anything like that.”