The Foreign Ministry made the statement on Saturday, days after a local rescue agency said it was rammed by a Chinese vessel.
Vietnam and China have long been embroiled in maritime disputes in the potentially energy-rich stretch of water.
The boat sank on Wednesday near Da Loi island in the Paracel Archipelago, the ministry said in an emailed statement. It said all five fishermen on board were rescued by another Vietnamese fishing boat.
"Vietnamese authorities are continuing to clarify the cause of the incident," the ministry said, without elaborating.
On Wednesday, Vietnam's national search and rescue agency said the boat had been rammed and sunk by a Chinese vessel. It did not say if the latter was civilian or military.
A spokesman for the foreign ministry in Beijing was cited by Chinese media as saying on Thursday that the fishing boat had sunk when the Chinese vessel approached, and that the Chinese crew had rescued the fishermen.
China claims 90 percent of the East Sea, where it has steadily expanded military and other installations on artificial islands and reefs, unnerving the region and angering Washington.
In addition to Vietnam, the Philippines, Malaysia, Brunei and Taiwan also claim parts of the sea.