The regional hospital in the northern Czech city of Liberec confirmed the new Omicron strain of Covid-19 in a female patient, its spokesman Vaclav Ricar told Czech Television Saturday.
"My colleagues from the department of genetics and molecular diagnostics confirmed the strain with 90-percent probability after a sequence analysis," said Ricar.
"Given where the patient came from and all the circumstances, we can confirm the strain has been confirmed," added Ricar.
He said the sample would now be analysed by the national reference laboratory.
"But the result is already very precise," Ricar said.
Babis said the woman was vaccinated and had mild symptoms of the disease.
The Czech Republic, an EU member of 10.7 million people, is currently grappling with a spike in Covid-19 infections making it one of the worst-hit countries in the world in terms of infections per capita.
Overall, the Czech Republic has seen more than 2.1 million confirmed Covid-19 cases and 32,744 deaths.
EU officials agreed on Friday to urge all 27 nations in the bloc to restrict travel from several southern African nations.
The Czech Republic already imposed restrictions on travel from the region on Friday.