The German Foreign Ministry has criticised the move, saying that "nothing about their work can warrant or justify such a serious step."
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Russia on Wednesday designated three German non-governmental organisations as “undesirable,” a move that drew sharp criticism from Berlin.
The Prosecutor General's office said that the organisations' activities “threaten the foundations of the constitutional order and security of the Russian Federation.”
Russian authorities have already designated more than 30 foreign groups as “undesirable” organisations in line with a law that has been widely seen as part of the Kremlin's efforts to stifle criticism.
Two of the affected organisations were involved in the St. Petersburg Dialogue, a German-Russian forum bringing together civil society groups, think tanks and decision-makers from the two countries.
“To ban the work of organisations that strive for understanding between our two countries and peoples is a serious setback for our efforts to achieve better relations with Russia,” said German Foreign Minister Heiko Maas.
“Nothing about their work can warrant or justify such a serious step,” said Maas. “I urge Russia to reverse this step and encourage the free exchange within civil society. Representatives of civil society must be allowed to do their work without being criminalised.”