Energy prices for the manufacture of glass have played a role in the shortage, as has the ongoing conflict in Ukraine, which supplies German brewers with glass.
Russian blockades of Ukrainian ports have also hampered exports out of the country, threatening a global food crisis that could become catastrophic.
"It is deadly for small brewers," Stefan Fritsche, who runs a German brewery, told the Times, citing difficulties in getting customers to lug their empty crates back to the stores.
In a statement sent to Insider, general manager of the German Brewers' Association, Holger Eichele, said the shortages were "indirectly related" to the conflict in Ukraine.
"It is a fact that unfortunately several glass factories in Ukraine have been destroyed by Russian attacks or had to close down and therefore can no longer deliver to Western Europe. This has increased the overall demand for glass products and glass containers in Germany as well," the statement added.
Eichele also cited reduced activity at factories as a result of rising energy costs as a reason for the shortages, which was also pushing up the price of glass bottles.
Breweries without supply contracts are paying 80% - 90% more for new bottles than they did last year, Eichele added in the statement.
The manager said there was no indication that beer production would be curbed, but added that it was becoming harder for brewers to "maintain the supply chain."
Breweries are tapping into Germany's deposit system to encourage more customers to return their empties. Under the system, buyers pay a deposit of either 8 or 15 euro cents (around $0.08 - $0.15) for a returnable glass bottle, which they can later claim back, often in the form of store vouchers.
Most people allow bottles to accumulate before returning them and redeeming their money in one go.
"The climate-friendly reusable system in Germany is unique in the world. Unfortunately, it is also uniquely expensive at present," Eichele said.
Some breweries have thought about upping the surcharge to persuade more people to return their empties, while other have been forced to increase the price of a crate of beer, the Times added.
"Every empty crate that comes back prevents us from having to buy a new one," a representative for one brewery told The Times.
The conflict has also increased the cost of other commodities and raw materials produced in Russia and Ukraine. This includes fertilizer, wheat, and sunflower oil — as supplies from both countries have been slashed.