Four people were transported to a local hospital, spokesperson Hunter Schnabel said.
A Coast Guard cutter and a helicopter were searching for the missing, Schnabel said.
Two children were believed to be among them.
US Coast Guard Petty Officer Chris Sappey said it was unclear where the boat was coming from before it flipped about 56km north of the Mexico border.
He described the vessel as a panga.
Pangas are open fishing boats commonly used by smugglers.
"They were not tourists," Sappey said.
"They are believed to be migrants."
The US Coast Guard said in a post on the X social media platform that it was searching off Del Mar, California, about 32km north of San Diego, after receiving a report of an overturned vessel.
The boat was found on the beach about 6.30am.
Nick Backouris, a lieutenant with the San Diego Sheriff's office, said his office helped with victims on the beach.
"The deputies were assisting with life-saving measures," he said.
with AP
