The Taiwanese factories were mistaken for Chinese after government sanctioned protests turned ugly, reportedly killing at least one person, with Reuters suggesting the number was as high as 21.
The riots were in response to China National Offshore Oil Corporation's placement of its $US1 billion ($A1.07 billion) HD-981 drilling rig into a heavily disputed region of the South China Sea.
China chartered a plane with medical supplies onboard as well as China Southern Airlines flights from Vietnam to collect 307 Chinese nationals caught up in the riots.
Four ferries were also commissioned to pick up about 4000 people from Vung Ang port, while others fled to Cambodia.
According to Vietnamese officials, the situation in the riot-affected provinces is stable but the country is adamant it will defend its perceived sovereign right to the disputed territory and has again asked for the Chinese rig to vacate the region.
Dozens of ships from either side are present around the rig, with allegations of intentional collisions levelled by both countries.