Buses, trams and underground trains are expected to remain in depots across many municipal transport companies due to the industrial action.
The state of Brandenburg estimates the outbreak caused some €8 million ($9.1 million) in damages, with farmers forced to kill numerous animals.
Founded in 2013, the Third Way political party is known for its nationalist, anti-immigrant and anti-Semitic ideologies and is widely described as neo-Nazi.
Mayor Michael Groubert of Kleinmachnow said professional animal trackers would also be deployed.
A spokesperson for the fire brigade said the situation was very tense as about 600 residents were evacuated from their homes.
The raid is part of an investigation into organised crime, arms, drug trafficking, and extortion
