"Etihad Airways this morning filed a request for a provisional injunction in order to protect its codeshare flights with Air Berlin," it said in a statement.
The Abu Dhabi-headquartered airline said it could no longer "wait for the German government to decide" whether to allow these codeshare flights to 29 destinations in Europe, the United States and the United Arab Emirates.
This is because the coming winter plane schedule is about to take effect on Sunday, running until next March, and some 82,000 flights are affected, it said.
The German Transport Ministry said Wednesday that a treaty between Germany and the UAE does not include a blanket authoritisation of codeshare flights.
Etihad holds a 29 percent stake in Air Berlin, and is its biggest shareholder.