Lameldin Abdelrahim, 62, is a paraprofessional at Public School 200K in Bath Beach.
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Authorities say other school personnel observed him sitting inside a cafeteria with a 5-year-old boy, whose head was allegedly in Abdelrahim's lap in an inappropriate manner.
Abdelrahim was questioned by detectives from the Special Victims Unit and faces multiple charges in connection to the incident, including sex abuse, sexual contact with an individual less than 11, acting in a manner injurious to a child less than 17 and sexual abuse of a child less than 14.
Police are looking at the suspect's prior employment history. He has no previous criminal record.
The New York City Department of Education released a statement, reading, "These allegations are deeply disturbing -- this individual was immediately terminated and is no longer eligible to work in our schools. Safety always comes first and we are providing the school community with additional support."
Some parents said they were outraged the school didn't notify them.
"I had no clue," one mother said. "That's shocking. Wow."
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"Nobody tells me," another said. "Nobody notified by email or phone call or text message."
"Obviously it's a concern," said another. "You expect that a school will be a safe environment."
Bail was set at $60,000.