The incident happened shortly before 7 a.m. in waters about 175 yards from Beacon's Beach, leaving the teenager with traumatic injuries to his upper torso, said Capt. Larry Giles of the city's Marine Safety department.
The victim went into surgery and is listed in critical condition.
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According to the captain, the water was about 9 feet deep at the location where the violent encounter occurred. Three good Samaritans rushed to the injured boy's aid and transported him to the shore on a kayak.
Encinitas lifeguards and sheriff's deputies who were in the area responded to the scene and a rescue helicopter was summoned.
A witness's video shows the chopper landing on the sand as emergency personnel attend to the teen, who was carried away from the water on a stretcher.
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The victim, who suffered multiple shark bites, was medevaced to Rady Children's Hospital in San Diego, according to a spokesperson for the medical center.
He was bitten by the shark while free diving on the first day of lobster season.
Beaches in the area were closed after the incident and will remain so for at least 48 hours, Giles said at a morning news conference.