The threats "are an attempt to undermine our support for Ukraine and test our unity", the ministry said in a post on X.
"Our response is clear: we will not be intimidated. Such threats and all forms of espionage in Germany are completely unacceptable."
The ministry did not specify the "threats" and would not provide additional details when asked by AFP. The Russian embassy declined to comment to AFP.
Russia's defence ministry last week published a list on its official Telegram channel containing 21 companies Moscow considers either subsidiaries of Ukrainian defence companies or suppliers of key components.
At least three German firms were among those listed as supplying unmanned aerial vehicles (UAVs) for Ukraine. The post included a vague suggestion that those locations could be targeted.
"The European public should not only clearly understand the underlying causes of the threats to their safety, but also know the addresses, as well as the location of 'Ukrainian' and 'joint' companies producing UAVs and their components for Ukraine in their countries," the Russian ministry wrote in last Wednesday's post.
On Monday morning, Russian authorities arrested a German woman accused of being part of an alleged Ukrainian-backed plot to blow up a services facility.
Russia's FSB security agency said the woman was arrested in the Caucasus city of Pyatigorsk with an explosive device in her backpack.
A German foreign ministry spokesman said they were aware of press reports about the arrest but would not comment further out of privacy concerns.
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