Germany's first two cases of the Omicron variant have been confirmed in Munich, the Bavarian health minister says.

Omicron, first detected in South Africa in November, has been classified as a "variant of concern" by the World Health Organisation.

The European Centre for Disease Control has said that the strain could significantly reduce the effectiveness of the available vaccines and increase the risk of reinfection.

The two travellers found to be carrying the strain in Germany had entered the country by plane from South Africa on November 24, Bavarian Health Minister Klaus Holetschek said on Saturday.

They had sought out tests for themselves after reading media coverage of the growing concerns surrounding the new strain, Holetschek said.

According to virologist Oliver Keppler, genome sequencing for the cases was still pending, but it had been "proven beyond doubt that it is this variant".

Another suspected case was reported in the state of Hesse on Saturday. That also involves a traveller from South Africa, state social minister Kai Klose said, adding that tests had reveals several mutations typical for this variant.

The Bavarian health ministry urged passengers who arrived from South Africa on the same flight on November 24 to immediately contact their health authorities.

All people who have arrived from South Africa in the past 14 days have been urged to immediately reduce their contact with others, take and a PCR test, while reporting their travel history to officials.

In addition, all persons arriving from parts of southern Africa classified by Germany's national disease control agency, the Robert Koch Institute, as "areas of variants of concern" must quarantine for 14 days, regardless of their vaccination status.

"We must do everything we can to prevent the spread of the new variant in (Bavaria) and in Germany," a state ministry spokeswoman said.