The temporary border controls and certain entry restrictions will start Sunday at midnight, dpa reported.
It was not clear for how long the border controls would last.
Bavaria Governor Markus Soeder, whose state borders both Austria and the Czech Republic, said earlier Thursday that if the federal government designated the Czech Republic and Austria’s Tyrol region as mutation areas, Bavaria would request permission to erect border posts where travelers who don’t present a negative COVID-19 test would be turned away.
Soeder said all the regions of Bavaria with high coronavirus infection rates, except for one, are located on the German-Czech border.
He praised measures taken by the Czech Republic to contain the spread of virus variants and criticized authorities in Tyrol, saying they appeared not to be taking the issue seriously.
Chancellor Angela Merkel and the governors of Germany’s 16 states agreed late Wednesday to extend the country's current pandemic lockdown until at least March 7, in part due to fears over more contagious variants.
Schools and hairdressers will be able to open earlier, albeit with strict hygiene measures.
In a speech to Parliament on Thursday, Merkel defended her government's decision to set a lower infection target for easing the lockdown further: a number of new weekly cases per 100,000 inhabitants below 35.
“The virus doesn’t follow dates, the virus follows infections numbers,” she told lawmakers.
Germany’s disease control agency said there were just over 64 cases per 100,000 inhabitants nationwide in the past week, down from over 200 before Christmas.
The Robert Koch Institute on Thursday added 10,237 new confirmed COVID-19 cases and 666 deaths to Germany's totals, bringing the country's overall case count since the start of the pandemic to 2.31 million and the death toll to 63,635.