Germany ambassador Martin Erdmann had already been called in by the Turkish foreign ministry on Saturday over a rally that Ankara said was organised by supporters of Kurdish militants in Cologne.
Turkish state-run news agency Anadolu said the summons related to a previous incident where Erdmann had been unable to attend but did not specify further.
A Turkish foreign ministry source, who asked not to be named, said it was a "coincidence" that the latest summons came so soon after the previous order from the ministry at the weekend.
German foreign ministry spokesman Martin Schaefer confirmed the summons, saying it was the 17th time in his tenure as ambassador that Erdmann had received such an order.
Erdmann has been Berlin's envoy to Ankara since August 2015.
Schaefer told reporters in Berlin the number of summonses Erdmann had received was "very unusual" between "partners within NATO".
Relations between the allies deteriorated sharply after last year's failed coup, with Berlin condemning the mass arrests in Turkey which have included German citizens.
Among those imprisoned is Deniz Yucel, a German-Turkish journalist with the Berlin-based newspaper Die Welt, accused of terror charges earlier this year.
But Turkey has repeatedly accused Germany of supporting "terrorists", referring to the outlawed Kurdistan Workers' Party (PKK) and individuals accused of involvement in the failed coup.
The Turkish foreign ministry said on Saturday it expressed "in a strong way" its opposition to the rally which it claimed was "an activity by the PKK terror group's extensions in Germany and their spreading terror propaganda there today in Cologne".
Erdogan has accused Germany of "Nazi" and "fascist" practices while Germany has responded by updating its travel advice to warn citizens that they could face arrest if they travel to Turkey.
The PKK, which has waged an insurgency inside Turkey since 1984, is proscribed by Turkey as well as the European Union and the United States.
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