A multinational search for 14 people who remain missing was still under way on Tuesday afternoon involving Vietnamese, Philippine and Chinese rescuers.
Vietnamese authorities announced on Monday that three more of the 62 people on board had been saved but did not provide details.
The Vietnamese cargo vessel Khoi Nguyen 18 sank late on Saturday near Fiery Cross Reef, a Chinese-built island and military outpost in the hotly contested Spratly Islands.
The vessel went down while operating in bad weather in the East Sea, the Vietnamese foreign ministry said, adding that all 48 rescued people had been transferred to Vietnamese authorities, who were providing medical care before taking them back to the mainland.
Vietnam said it mobilised rescue operations immediately while co-ordinating closely with Chinese rescue ships, helicopters and other vessels in the area also joined the search.
The Philippine Coast Guard, which deployed a patrol vessel and an aircraft after receiving a request from Vietnam, said the operation was being carried out under international maritime agreements and bilateral cooperation with Vietnam.
China has become increasingly aggressive in asserting its claims in virtually the entire South China Sea, through which about $US5 trillion ($A7.2 trillion) in global trade transits each year.
Vietnam, Malaysia, Brunei and Taiwan also have overlapping claims in the strategic waterway along with China and the Philippines.
