According to the Hawaii County Fire Department, the incident occurred early Monday morning. A lava bomb punctured the roof of the boat, leaving a large hole in the vessel and damaging one of the boat's railings.
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The boat managed to return to Wailoa Harbor in Hilo around 7 a.m. with the twelve passengers - all with varying degrees of injuries.
Of the 12 injured passengers, three were taken by ambulance to Hilo Medical Center. Two passengers were in stable condition. One, a woman in her 20s, was in serious condition with a fractured femur. The remaining nine passengers drove themselves to the hospital, and the fire department reported that their injuries were superficial.
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Kua 'o Ka La Public Charter School was destroyed by lava last week, along with nearby Ahalanui Beach Park.
ABC News contributed to this report.