Major airports will also be outfitted to detect and defend against unmanned aerial vehicles, the interior ministry said.
The federal police unit will have "a clear mandate to detect, defend, intercept and, if necessary, shoot down drones," Interior Minister Alexander Drobrindt said at a ceremony near Berlin.
"We cannot accept that hybrid threats using drones remain a danger to our security," he added.
Dobrindt said Germany is investing more than 100 million euros ($116 million) in drone defence technology over the coming year, and plans to grow the new police unit to more than 130 officers.
Germany and other European countries have experienced a slew of suspicious drone incidents in recent months.
Russia has been blamed for many of the drone incursions, which have flown over sensitive locations such as airports, military bases, ports and power plants.
Dobrindt said Germany plans to announce a new joint drone defence centre later this week that will coordinate responses between federal police, local authorities and the military.
German lawmakers this year gave the police broader authority to shoot down drones if necessary.
The government has also proposed giving the military a greater role responding to potential drone threats in German airspace.
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