Officials say their investigation has also uncovered nude photos of another girl, just 13 years old, sent to the teacher's iPhone.
Parents with whom we spoke were outraged. They are furious that a man who once taught children at their school is accused of having sex with one of his female students and having inappropriate contact with others.
Authorities identified the teacher as 46 year-old Wayne Bartley.
"We went to three schools where he was a teacher and each school we found a girl that he had an inappropriate relationship with," Richard Condon, special schools investigator, said.
Investigators say Bartley had sex with one thirteen year-old student at a motel in the Bronx twice a month for more than a year.
From 2005 to 2008, Bartley was a science teacher at I.S. 229 in the Bronx.
He then transferred to I.S. 392 in Brooklyn before he was "discontinued" by administrators for an unspecified reason.
He taught science at Kipp Amp Charter School in Brooklyn last year.
According to investigators, he told another student, "that she was very pretty. His favorite. He told her that he wanted to take revealing photographs of her. The student replied that she had a two-piece bathing suit with a wraparound skirt. Bartley told student that was too much clothing and asked her to pose for him nude."
Investigators say the girl later sent a series of nude pictures to Bartley's cell phone.
"He should get arrested. We would think he'd get arrested," Condon said.
The case has been forwarded to the Brooklyn and Bronx District Attorney's Offices to determine whether charges should be filed.