Diyanet, which oversees religious activity in Turkey, on Wednesday voiced distaste over the Berlin mosque where men and women pray side-by-side, saying it was incompatible with the principles of Islam.
Diyanet's criticism sparked strong words from Germany, with foreign ministry spokesman Martin Schäfer firmly rejecting the Turkish agency's comments "which are targeted at limiting people's right to practise their religion and freedom of opinion".
"How, where, when and in which manner people worship is not a matter for the state," said the spokesman.
"According to our understanding, the state has absolutely no authority over the assessment of theological questions. Rather, it has the duty to protect freedom of religion as well as freedom of opinion or press," stressed Schäfer.
Interior ministry spokesman Tobias Plate added that comments that "endanger domestic peace in Germany is something that cannot be accepted."
"We will be sure to express that bilaterally in every channel of dialogue that the interior ministry is responsible for," he added.
Berlin's new mosque, located in a rented room on the third floor of the Protestant Johanniskirche (St. John's Church) building, welcomes all Muslims - Sunni or Shia, Alawite or Sufi, and comes complete with female imams.
Ties between Ankara and Berlin have been strained since the failed coup in Turkey, and tensions have worsened over multiple issues including a referendum campaign to expand President Recep Tayyip Erdogan's powers.
Relations plunged further after Turkey imprisoned Deniz Yucel, a German-Turkish journalist with Germany's Die Welt daily, on terror charges earlier this year.