The incident happened before dawn on Monday about 160 kilometres (100 miles) northwest of Scarborough Shoal, off the Philippines' main island of Luzon.
The fishing vessel was moored to a floating device known as a payao, which is used to catch fish.
"The mother boat submerged, resulting in the death of its three crew members, including its boat captain," the coast guard said in a statement.
Eleven other crew members used smaller fishing boats to retrieve the bodies and took them to Infanta municipality in Pangasinan province.
The coast guard said the commercial vessel involved in the incident was foreign flagged, but did not specify from which country.
A crude oil tanker vessel called the Pacific Anna and registered under the flag of the Marshall Islands was in the area at the time of the incident, the coast guard said, after cross-checking the fishermen's account of the incident with marine traffic.
The coast guard said the vessel would be boarded by authorities at its next port.
The South China Sea has some of the world's most important shipping lanes through which trillions of dollars in trade passes annually.
President Ferdinand Marcos said the coast guard was investigating the cause of the incident and urged the public to "refrain from engaging in speculation".
Scarborough Shoal has long been a source of tension between Manila and Beijing.
China seized the ring of reefs from the Philippines in 2012 and has since deployed patrol boats in the area.
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