The operation would see about 100 officers from the Bavarian police support the federal police.
The operation would see about 100 officers from the Bavarian police support the federal police which was responsible for border controls in its efforts to monitor the A8, the A93 and the A3 motorways.
Bavarian Interior Minister, Joachim Hermann, and his counterpart from Austria, Wolfgang Sobotka, were expected at the A8 checkpoint later to speak to members of the police about the operation.
Border controls between Germany and Austria were reintroduced in 2015 amid large influx of refugees travelling to Western Europe via the western Balkans.
Bavaria, which is governed by the conservative Christian Social Union (CSU), bore the brunt of refugee arrivals due to its borders with Austria and the Czech Republic.