The Chinese government has already evacuated more than 3,000 people, Chinese state-run media report.
The first ship set sail on Sunday, while 16 critically injured Chinese nationals left Vietnam on a chartered flight, Xinhua news agency said.
Two Chinese workers have been killed and dozens more injured in unrest over a Chinese oil rig in disputed waters.
On Saturday the Vietnamese government called for an end to the protests.
Officials said “illegal acts” would be stopped as they could damage national stability.
However, dissident groups have urged people to rally again in major cities on Sunday and the authorities broke up some anti-China protests in Hanoi and Ho Chi Minh City.
In recent days crowds have set fire to at least 15 foreign-owned factories – including Chinese, Taiwanese and South Korean businesses – in several Vietnamese industrial parks.
Correspondents say the attacks appear to have worried authorities, as Hanoi depends heavily on foreign investment for economic growth.
However, China has urged authorities to take tougher measures to punish rioters.
“We are strongly dissatisfied by the Vietnamese side failure to respond effectively to curb an escalation,” Xinhua quoted security chief Guo Shengkun as saying on Saturday.
The protests have been triggered by China’s decision to move its Haiyang Shiyou 981 oil rig into contested waters in the South China Sea.
This led to confrontations between Vietnamese and Chinese ships earlier this month, as Vietnam sought to block the move.
China insists it will continue drilling in the area, west of the Paracel Islands – which are controlled by China but also claimed by Vietnam, and Taiwan.
Nationalist sentiment is currently running very high in Vietnam over the issue, correspondents say.
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