Turkish European Union Affairs Minister Egemen Bagis told reporters on Thursday that Germany's resistance to opening a new chapter in EU accession talks was linked to Chancellor Angela Merkel's "election campaign".
"That is unacceptable," German ministry spokesman, Andreas Peschke, told reporters.
Peschke said that Foreign Minister Guido Westerwelle summoned the Turkish ambassador around midday Friday "due to remarks from Turkish officials toward Germany".
"These remarks met with great disbelief here," Peschke said. "We will make our position abundantly clear."
It was not immediately clear who would meet the ambassador as Westerwelle was on an official visit to Ukraine.
Bagis had reacted angrily to news from Brussels that EU member states had failed to reach the necessary consensus on opening a new negotiating chapter with Turkey, which could have marked an upswing in ties.
An EU diplomat had said that Germany and the Netherlands "expressed reservations" at Thursday's closed door talks between EU ambassadors.
"If Merkel is looking for material for her election campaign, it should not be Turkey," Bagis told reporters, referring to the general election in Germany slated for September.
Merkel said Monday that she was shocked by Turkey's violent crackdown on protests in major cities, saying it "was much too harsh".
Peschke said there was "no direct link" between Ankara's response to the demonstrations and the EU negotiations because the chapter in question dealt with "technical issues", but he confirmed that Germany "and other countries" had expressed reservations on Thursday.
And he noted that "of course accession negotiations take place in a political context".
In February Merkel indicated she backed the opening of the new chapter, while warning that she was "sceptical" about the outcome of the negotiations.
Her deputy spokesman Georg Streiter insisted on Friday that neither Merkel nor her government were "questioning the accession process".
"This is not about whether but rather how to move forward with the accession process," he said.
He added that the EU wanted to continue working together with Turkey "also in the area of human rights".
However the leader of Merkel's Christian Democrats' parliamentary group, Volker Kauder, said Friday that the crackdown could have serious consequences for Turkey's EU ambitions.
"I can only warn [Ankara] against sending in the military" against protesters," he told the daily Die Welt in an interview to be published on Saturday.
"That would push Turkey light years away from Europe. Then the EU would have to suspend accession negotiations."
The Turkish government threatened this week to send in troops if the demonstrations continued.