The incident took place around 9:56 a.m. local time, when a call came in from a commercial vessel that reported there was another boat in trouble near Point Loma leading into San Diego Bay, according to Rick Romero of the San Diego Lifeguard Services.
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3 killed, 27 hospitalized after boat capsizes off San Diego coast
The initial report said there was just one person aboard the distressed ship. However, rescuers said there were as many as 30 people involved. James Gartland, the lifeguard chief for the city of San Diego, said the vessel hit a reef and broke.
"There are people in the water drowning, getting sucked by currents, people on shore," Romero told reporters at a news conference.
Seven people were in the water, and two had drowned, according to Romero. The remainder of the passengers, including one who was rescued from a cliff, were taken to area hospitals with conditions ranging from "hypothermia and injuries from the vessel breaking," Romero said.
At least three people needed CPR, according to Gartland.
Weather conditions, which caused the boat to break apart, also hindered the rescue efforts, according to a source with knowledge of the investigation. There were seven-foot swells, low clouds and some rain.
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Divers could not go in the water because the weather was so bad, the source told ABC News. However, crews were still searching for victims as there was not an official record of the number of people who were aboard the boat.
"I would have thought there were four people on that boat, you know there weren't a lot of people, four to six people on that boat," said witness Michael Jacobson. "And then all of a sudden, bodies just started coming up and jumping off, and it started tipping, tipping quite a bit."
The U.S. Customs and Border Protection is investigating the crash since it took place in federal waters.
Jeff Stephenson, a Border Patrol agent, told reporters that the boat was a smuggling vessel, and the likely operator was in custody.
"(Smugglers) don't care about the people they're exploiting, all they care about is profit. To them, these people are just commodities," Stephenson told reporters.
WATCH: Officials give update after boat capsizes off San Diego
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3 killed, 27 hospitalized after boat capsizes off San Diego during possible human smuggling operation
Sharp Memorial Hospital and Sharp Grossmont Hospital reported receiving eight patients from the incident, with injuries mostly coming from passengers hitting rocks in the ocean, a spokesperson said in a statement. Three of the patients from Sharp Grossmont Hospital are expected to be discharged, while the remaining patients were in stable condition, the hospital said.
A spokesperson for UC San Diego Medical Center, Hillcrest said it also received eight patients, three of whom were trauma patients while the others were sent to the emergency department.
On Sunday night, the U.S. Coast Guard said in a statement that 29 had reportedly been accounted and four others were dead, but an updated statement Monday said three were dead and of the 29 survivors, five remain in the hospital.
All but two people on the boat were Mexican citizens without legal status in the U.S. The others were a Guatemalan citizen without legal status in the U.S. and a U.S. citizen who was identified as the pilot, U.S. Customs and Border Protection said Monday. Among the 28 in CBP custody were a 15-year-old boy traveling alone and 21 men and six women, ages 18 to 39.
The Associated Press and ABC News' Chris Barry, Michelle Mendez and Sarah Hermina contributed to this report.