State Secretary of the German Foreign Office, Markus Ederer, called his Turkish counterparts and declared that freedom of the press and of expression are "not negotiable," a spokeswoman for the foreign office said on Wednesday.
Ankara was incensed when broadcaster NDR's satirical show extra3 showed a video of a song criticizing Turkish President Erdogan earlier this month, called "Erdowie, Erdowo, Erdogan".
Turkey's government was so appalled by the video that German Ambassador to Ankara Martin Erdmann was formally summoned to the Foreign Ministry twice to explain the broadcast.
DPA learned that officials demanded the video never be shown again.
But German officials have defended the video, with another government spokeswoman also saying that Chancellor Angela Merkel emphasized the importance of freedom of expression.
European Commission head Jean-Claude Juncker also chided Turkey for its reaction to the video, with his spokeswoman saying on Wednesday that Juncker "does not appreciate this movement of calling in the German ambassador just because of a satirical song."
"He believes this moves Turkey further from the EU rather than closer to us," Juncker's spokeswoman Mina Andreeva said.
"While he appreciates our shared cooperation and shared interest in tackling common challenges this move does not seem to be in line with upholding the freedom of the press and freedom of expression which are values the EU cherishes."
Turkey, a long-standing candidate for EU membership, had also recently negotiated a deal with the EU to take back all migrants landing on the Greek islands in exchange for European concessions including cash and an agreement to speed up Turkey's membership bid.
But the deal has sparked criticism that the 28-nation bloc sold out its principles in a desperate bid for Ankara's help, especially after a crackdown on media that oppose Erdogan.
Turkish authorities recently took over top-selling newspaper Zaman, which opposes Erdogan, garnering condemnation from German and other international leaders.
Magazine Der Spiegel announced earlier this month that it had been forced to withdraw its Istanbul correspondent due to the country's treatment of the press.
"Journalists are being arrested, there are absurd court trials against media representatives, and newsrooms are being placed under state control," the German Journalists' Union said in a statement on Tuesday.