Russia's Foreign Ministry summoned the chargé d'affaires at the German embassy in Moscow on Wednesday to protest sanctions announced by Berlin over an explosives-laden drone found at Leipzig airport.
The diplomat was summoned over what the ministry characterized as anti-Russian actions and statements by the German leadership.
Video footage showed the chargé d'affaires arriving with the head of the embassy's political section before entering the Foreign Ministry building.
Germany's new ambassador to Russia, Clemens von Goetze, was reportedly not in Moscow.
Moscow denies any involvement with the drone found at Leipzig/Halle Airport on August 4. Russia has described the incident involving the device, which failed to detonate, as a "provocation" serving the interests of militaristic circles in Europe and Ukraine.
German Interior Minister Alexander Dobrindt and Foreign Minister Johann Wadephul on Tuesday publicly blamed Russia for the drone incident and announced punitive measures.
Wadephul said the Russian consulate in Bonn would be closed and that an agreement covering the Russian House cultural centre in Berlin would be terminated.
Russia has promised to take retaliatory measures.
Possible steps could include the closure of the Goethe Institute, Germany's state-supported cultural body that promotes the German language and cultural exchange abroad, as well as the German consulate general in St Petersburg.
Germany and Russia have previously closed each other's consulates in the course of tit-for-tat measures.