Berlin pushed back, denying Moscow's claim that the centre housing military personnel from Germany and its NATO allies violates the treaty that allowed Germany's 1990 reunification.
Germany on Monday inaugurated the centre in the port city of Rostock in the formerly communist east to boost defence readiness in the Baltic Sea region as Russia pursues its Ukraine offensive.
The Russian foreign ministry said Tuesday it had expressed a "decisive protest" to the ambassador over the creation of the centre.
It said in a statement that "in Washington, Brussels and Berlin, they must realise that the expansion of NATO military infrastructure in former East Germany will have the most negative consequences".
Moscow warned that this "will not remain without a corresponding response from the Russian side".
The foreign ministry said the new centre was a "blatant breach" of the treaty on the reunification of Germany in 1990 that said no foreign armed forces would be deployed in the area.
The centre will be led by a German admiral and manned by staff from 11 other NATO countries, according to the German defence forces.
It will aim to "coordinate naval activities in the region" and provide NATO with a "maritime situation picture in the Baltic Sea region around the clock".
A German foreign ministry spokesman told AFP that its ambassador had "very clearly denied that the 2+4 Treaty had been violated".
The 2+4 Treaty was agreed between the former West and East Germany and the four powers that occupied Germany at the end of World War II -- the then Soviet Union, the United States, France and Britain.
The ministry spokesman said that deployment of German armed forces to NATO structures "is expressly permitted under the 2+4 Treaty," including in the former East Germany and long-divided Berlin.
"As in the past, the command staff in Rostock will consist of both German soldiers and foreign exchange and liaison officers. It will thus make a contribution to the NATO Readiness Forces."
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