In a news conference Tuesday morning, Durham Police Chief Jose Lopez said Officer Samuel Duncan had arrested the teen - identified as Riverside High School student Jesus Huerta - on a warrant for second-degree trespassing, and was bringing him to the Durham Police Department headquarters building off West Chapel Hill Street and South Duke Street.
Lopez said Duncan was driving in the building's parking lot around 2:30 a.m. when he heard a loud noise from the back seat of the car and jumped out of the vehicle.
The cruiser then rolled into a parked van and came to a halt. Huerta was found dead in the back seat.
Chief Lopez said Tuesday the cause of death has not been determined, but sources tell ABC11 the boy died of a self-inflicted gunshot wound.
In his news conference, Lopez did not take questions. He did not say if a weapon was found or if Huerta was searched before he was placed in the backseat of the cruiser.
"It does not appear that a Durham police officer fired a weapon during this incident," Lopez said.
ABC11 spoke with Huerta's brother Tuesday, who told us he does not believe his brother owned a gun.
Lopez said Duncan joined the department in July 2012. He has been placed on administrative leave with pay, which is standard procedure.
"I want to reassure the community that this incident is being thoroughly and completely investigated in an effort to determine exactly what happened," said Lopez.
"Our thoughts and prayers are with the Huerta family during this difficult time," Lopez continued.
An autopsy will be conducted to determine exactly how Huerta was wounded.
Huerta is no stranger to police. He was arrested earlier this year for possession of burglary tools.
Meanwhile, ABC11 has obtained a copy of the police department's policy for transporting and handling prisoners.
Among other directives, it states that "a transporting officer will search the prisoner, making sure no weapons or contraband were overlooked. The officer should never assume another officer made a search."
It also says Durham officers are prohibited from handcuffing a suspect to "any fixed or moveable object." They're also urged to "constantly monitor an arrestee."
Along with the SBI, the Durham Police Department's Professional Standards Division and Homicide Unit are reviewing Huerta's death.