"I strongly condemn the massacre during the morning prayers on behalf of the fundamental values of humanity that we have defended," Ahmet Davutoglu wrote in a message on Twitter.
Morsi's Muslim Brotherhood said today that 35 supporters were killed at dawn when security forces opened fire on them as they prayed.
The Islamist group's political arm, the Freedom and Justice Party, called for "an uprising by the great people of Egypt against those trying to steal their revolution with tanks."
"Egypt is the hope for the rising calls for democracy in the Middle East and Turkey will always be in solidarity with the Egyptian people," he added.
On Friday, Prime Minister Recep Tayyip Erdogan condemned the military intervention as anti-democratic and chastised the West for failing to brand Morsi's ouster a coup.