Three people have died after a crowded “smuggling vessel” hit a reef and capsized off the coast of San Diego on Sunday, officials said.

The U.S. Coast Guard said Monday that it has suspended its response after searching for survivors overnight.

Thirty-two people have been accounted for, the Coast Guard said. Twenty-nine people are alive, of which, five were taken to the hospital, with one of the five in critical condition, the Coast Guard said Monday.

The Coast Guard originally reported four deaths, but has since amended the number to three fatalities.

The crash took place shortly before 10 a.m. Sunday, 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. The vessel hit a reef and broke, said James Gartland, the lifeguard chief for the city of San Diego.

“There are people in the water drowning, getting sucked by currents, people on shore,” Romero told reporters at a news conference.

Some survivors were suffering from “hypothermia and injuries from the vessel breaking,” Romero said.

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.

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 only care about their pockets,” Stephenson told reporters.

The cause is under investigation, according to the Coast Guard. The U.S. Customs and Border Protection is investigating the crash since it took place in federal waters.

ABC News’ Chris Barry, Michelle Mendez and Sarah Hermina contributed to this report.