A junior at the elite Bronx High School of Science was busted with a prohibited cellphone in his lap while taking the US History Regents exam — and a whistleblower is accusing officials of botching the probe into whether the offender was part of a cheating ring.

David Suker, a teacher proctoring the exam, spotted the brazen teen “texting and looking at his iPhone while taking the exam” at around 9:45 a.m. Tuesday, he reported to Department of Education officials.

About 10 minutes later, Suker notified the teacher who arrived to relieve him.

That teacher confiscated the device, and the student was then hauled into a dean’s office, where he was ordered to unlock his phone.

He did — and then appeared to remove incriminating evidence, Suker told The Post.

“When he opened the phone, he immediately started deleting,” Suker said an eyewitness told him.

Under proper protocol, electronic devices confiscated from students during an exam should be handled only by officials pending a thorough investigation, according to people familiar with the rules.

A full review of the teen’s texts could show whether he was exchanging information or answers with other test-takers.

“They need to find out how many other kids were in on this,” Suker said. “Who was he texting — and what?”

Department of Education officials insisted the exam — taken by about 700 students that day at the school — was not compromised, and portrayed the incident as “ isolated.”

“No items were deleted,” a spokeswoman said. “There is no evidence that any texts were sent during the exam.”

The breach was reported to city and state authorities, and “disciplinary action is being taken,” officials said.

On the school intercom the morning after the test, an administrator announced, “A student was caught with an electronic device. If you’re caught with an electronic device you get a zero,” Suker said.

Bronx Science is one of the nation’s most prestigious high schools — eight alumni have won Nobel Prizes — and one of NYC’s eight specialized schools that admit kids who score the highest on a sole entry exam.

In a major cheating scandal at specialized Stuyvesant HS in June 2012, some 71 juniors were caught using cell phones to exchange answers on Regents’ exams through text messages.