The government said the evacuation would take four days and involve flights chartered to 11 different Vietnamese cities.
Vietnam, which has been praised for its pandemic response after reporting just 400 cases and no deaths, went back on high alert at the weekend as it confirmed its first local infections since April, all in the popular tourism destination of Danang.
An aggressive and widespread testing regime, plus a strict quarantine had helped the southeast Asian country almost eradicate Covid-19 within its borders, but the authorities are now grappling with its first internal infections for months.
Although foreign tourists are still barred from entering the nation, there has been a surge of domestic travel as the Vietnamese take advantage of discounted flights and hotel deals.
Anyone who had recently returned home from a break in Danang is required to quarantine at home for 14 days, the health ministry has said.
In addition, the prime minister Nguyen Xuan Phuc has also ordered police to step up a crackdown on illegal immigration.
It is not clear if the new Danang cases are connected to people entering Vietnam secretly but state media said on Sunday that police had arrested a Chinese man accused of running a gang which smuggled people into the country from China.
On Monday, the government announced more than 1,500 people had been caught illegally crossing the border from China into Ha Giang province in Vietnam since May.
Most of those caught were Vietnamese citizens and had been sent into quarantine.
The fist new case in Danang, known as Patient 416, entered hospital on 20 July with flu-like symptoms but is now on a ventilator and in critical condition, according to local media.
Concened officials have said they do not know how he caught coronavirus and he had not recently left Danang.
A hundred of his recent contacts were traced and tested but all were negative for the virus.
Now, three further cases have been confirmed, including a 17-year-old boy from a neighbouring province who had travelled on a coach with people from a Danang hospital.
As well as evacuating tens of thousands, the authorities are now reimposing other control measures such as closing hospitals, asking the public to wear masks again and suspending football matches.
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