Crew members pulled 25 people from the water, said the San Diego Fire-Rescue Department on Twitter. Officials said that 23 were injured and two died.
Chief Patrol Agent Aaron M. Heitke said the capsized boat was part of a “suspected maritime smuggling event.”
Federal officials are still searching the water in vessels and aircraft for anyone else in the water, according to the fire department.
Border Patrol officials told KPBS that the boat, which overturned off Point Loma, is suspected of being part of a human smuggling operation. And a San Diego fire official also said the boat was suspected of being used by smugglers to bring people illegally into the United States, according to the Los Angeles Times.
“It is very rocky over there, and the waves, while they weren’t too high, they looked pretty strong,” Jose Ysea, a spokesman with the San Diego Fire-Rescue Department, told the Union-Tribune.
Several Coast Guard vessels were deployed and were searching for victims, Supervisory Border Patrol Agent Jeffery Stephenson told the paper.
San Diego City Councilmember Jen Campbell, who represents the district including Point Loma, wrote on Twitter that she was monitoring the situation.
“While we wait for an official update, my thoughts are with those impacted and the many emergency personnel responding to the scene,” she added.
The boat overturned near Cabrillo National Monument, which is a park with trails, tide pools, and exhibits on California history, operated by the U.S. National Park Service. It is named after Juan Rodriguez Cabrillo, who stepped on shore in 1542 as the first European to arrive on what is now the West Coast of the United States, according to NPS.gov.
The Epoch Times has contacted the Department of Homeland Security for comment.
Reuters contributed to this report.