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According to their own statements, the federal police turned away significantly more people at the border with the Czech Republic than at the border with Tyrol.
Both are considered virus variant areas.
A spokesman for the federal police announced on request that there were around 1200 people at the border with Austria from Sunday to Tuesday, while at the border with the Czech Republic there were 7100.
The Federal Ministry of the Interior had previously announced that 37,362 people had been checked at both border sections.
Because of the border dispute, according to Czech Prime Minister Andrej Babis, the states of the Visegrad Group have called on the EU to intervene.
"What happens at the German borders is of course a violation of the internal market and a big problem for all of us," said Babis after a meeting with his colleagues from Poland, Hungary and Slovakia.
EU Council President Charles Michel was asked for help.
Federal Interior Minister Horst Seehofer (CSU) wants to find out about the controls on entry at the German-Czech border crossing on Autobahn 17 in Breitenau on Thursday afternoon.
All developments in the live ticker