Violent crackdowns have left hundreds dead and thousands more injured since Monday.
A foreign ministry spokeswoman said: "On the orders of Foreign Minister [Guido] Westerwelle, the ambassador was told the position of the German government in no uncertain terms.”
On Wednesday, Westerwelle urged all sides to renounce violence and return to negotiations to resolve the conflict that has cost the lives of at least 525 people.
And the repression by the Egyptian army on Morsi's Islamist supporters, the Muslim Brotherhood, has been met with criticism in Germany.
The Welt newspaper called for dialogue to avoid civil war but conceded, saying “the Islamists see no reason for talks.”
In the face of rising violence, magazine Der Spiegel attacked Barack Obama accusing him of being “powerless” to stop the fighting and failing to take a clear position on the conflict.
The US government provides $1.3 billion in annual aid to Egypt's military.