A student's father was among the victims killed in the shooting.
The New York Times says Gregory F. Sullivan has been suspended from his tenured position as humanities instructor.
According to an internal personnel document, Sullivan told the class: "If someone with orange hair appears in the corner of the room, run for the exit." He had just turned down the lights to show a documentary.
9NEWS has learned that the student is the son of 51-year-old Gordon Cowden, the oldest of the 12 people to be killed in the mass shooting. The suspect in the case appeared in court with bright orange hair after his arrest.
A spokeswoman for the Cowdens says the family wished to remain silent on this incident. Because of that 9NEWS is choosing not to name the student in our reporting.
Cowden was in the theater with two of his other children, who both survived the attack.
The Times reports the student left the room visibly upset, according to the document.
The newspaper says the academy on Kings Point, Long Island, informed Sullivan on Aug. 10 that he had 10 days to contest his dismissal.
The professor denied knowing he had a student in his class who had a connection to the shooting. The academy says a campus-wide email went out less than a week before the incident to inform people about the connection.
A spokeswoman for the Merchant Marine Academy did not respond to our questions about whether that email shared the student's name.
The academy has fewer than 1,000 students. It is a military-style campus run by the US Department of Transportation. It is a specialized college geared toward people who want a career on commercial ships.
Sullivan apologized to the students and faculty. He declined to comment to the Times.
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