in the central Poltava region, where they will be held in quarantine for 14 days.
President Volodymyr Zelensky urged the protesters to show empathy.
Ukraine's security service (SBU) said a fake email claiming to be from the health ministry falsely said some evacuees had contracted the virus.
SBU officials are now investigating the apparent hoax, a statement said.
Ukraine has no confirmed cases of the new coronavirus, which originated last year in China's Hubei province.
To show solidarity with the evacuees, Ukraine's Health Minister Zoryana Skaletska said she would be joining them in quarantine and would run her ministry by Skype.
"I hope that my presence there will calm those in Novi Sanzhary, as well as the rest of the country," she wrote in a Facebook post (in Ukrainian).
What happened in Novy Sanzhary?
On Thursday, 45 Ukrainians and 27 foreign nationals were flown from Wuhan in China, the epicentre of the deadly outbreak, to Kharkiv in eastern Ukraine.
Six buses then drove them to the health spa in Novi Sanzhary, where they were met by demonstrators lighting bonfires and hurling stones.
Armoured personnel carriers were seen deployed in the small town.
After a tense stand-off, police and the national guard manage to unblock the road to the building where the evacuees would be spending 14 days.
The country's health ministry said none of the passengers were sick.
Ukraine's diplomatic mission added that three Ukrainians and a resident of Kazakhstan had been left behind in China, because they had reported having a fever.
Prime Minister Oleksiy Honcharuk, Health Minister Zoryana Skaletska and Interior Minister Arsen Avakov all travelled to the city to try and calm tensions.
In footage published by local media, Mr Avakov was seen telling the protesters: "We are not talking about infected people, we are talking about healthy people."
One person then replied: "So far."