"Starting from today, the Bavarian border police is carrying out flexible control of our borders, and [doing] this with the most up-to-date equipment and technology," Soeder said on Twitter.
The new equipment includes drones, thermal imaging cameras and night-vision devices, according to Soeder.
According to media reports, the border police will begin its work with 500 personnel of the regional police.
The new regional police unit cannot act independently from the state. In particular, it cannot send any of the people it detains back to Austria.
German Interior Minister Horst Seehofer, the head of the Christian Social Union (CSU) in Bavaria, has been promoting a tougher border and migration policy.
In early July the German coalition government, including CSU, agreed to accelerate the returns of migrants, who applied for asylum in other EU countries, to where their demand was registered, but only if there were the necessary agreements in place with those countries.