From January 1 2013, the new GEMA system will take fees based on a percentage of a venue's ticket prices as well as its size. A 50% surcharge will also be introduced for events that last more than five hours, with a similar increase after three hours.
The agency claims that 60% of establishments won't see their payments increase, that clubs should be able to pay 10% of their ticket prices and that some establishments may actually see GEMA payments decrease.
But The Club Commission, which represents Berlin's nightlife industry says that "clubs are fearful for their existence" and that an average-seized club, which now pays 28,000 Euros (?22,456) a year could face bills of 180,000 Euros.
A campaign against the new fee system has already collected more than 200,000 signatures and 5,000 people demonstrated outside GEMA's summer party in Berlin at the end of last month. More than 2,000 clubs across Germany halted decks for five minutes to demonstrate their opposition to the plan.
The Guardian reports that Berghain, which has staged events lasting more than 48 hours, faces a 1,400% increase in fees and has said that a New Year's Eve event would be its last.
Watergate boss Steffen Hacks has also said that he will be forced to shut down, expecting bills of 200,000 Euros instead of 10,000 Euros and telling Die Tageszeitung newspaper "How is one supposed to operate as a free entrepreneur under these kinds of conditions?"
More than 10,000 tourists visit Berlin every weekend and 35% of them cite the city's nightlife as a big draw.
"It's dangerous not only for the clubs but for the whole of tourism, hotels, taxis, and whoever has something to do with the party industry," said Ingo Damm, who runs trance nights at Berlin's KitKatClub. "It's definitely a disaster for Berlin."