Germany partially closed its borders with the Czech Republic and Austria's Tyrol on Sunday over a troubling surge in COVID-19 variants, drawing a swift rebuke from the European Union.

A thousand police officers have been mobilised to ensure strict border checks, which recall the much-criticised early days of the pandemic when EU countries hastily closed their frontiers to each other.

At the Kiefersfelden crossing in southern Bavaria, officers in yellow high-visibility vests and wearing balaclavas to stave off the chill in -15 degrees Celsius (5 degrees Fahrenheit), meticulously stopped each vehicle coming from Austria.

Under the new rules, in place until February 17, only Germans or non-German residents are allowed to enter, and they must provide a recent negative coronavirus test.

Some exceptions are allowed for essential workers in sectors such as health and transport, as well as for urgent humanitarian reasons, the interior ministry has said.

German rail company Deutsche Bahn has suspended services to and from the affected areas.

At Frankfurt airport, the country's largest, federal police were on Sunday checking passengers arriving from Vienna and Prague.

The restrictions are aimed at slowing the spread of new, more contagious variants that first emerged in Britain and South Africa, and have created new virus hotspots along the Czech border and in Austria's Tyrol region.

Chancellor Angela Merkel's government recently decided to extend Germany's partial lockdown until March 7 because of the risks posed by the new strains, even if daily infection numbers have fallen over the past weeks.

In the Czech Republic, one of the hardest-hit countries in Europe, three cantons including two on the German border have been placed under lockdown due to the prevalence of the British virus variant.