The two countries announced late Thursday that they were recalling their ambassadors for consultations hours after Turkish Prime Minister Recep Tayyip Erdogan said Egyptian leaders should stand trial for the military's move against Morsi's supporters. More than 600 people died in the violence.
Erdogan also accused the West of ignoring bloodshed in Egypt and urged an urgent United Nations Security Council meeting.
Turkish President Abdullah Gul voiced more criticism Friday.
"I deeply feel the pain for every single Egyptian that was killed," Gul said, according to the state-run Anadolu Agency.
"All that happened in Egypt is a shame for Islam and the Arab World," he was quoted as telling reporters during a visit to Azerbaijan.
Turkey's Islamic-based government had strongly backed Morsi as an example for the Arab world of a democratically elected pro-Islamic leader and has strongly criticized his July 3 ouster. Turkey's ambassador to Cairo, Huseyin Avni Botsali, was summoned by Egypt's Foreign Ministry recently over the Turkish criticisms.
Gul rejected Egyptian accusations that Turkey was interfering in the country's internal affairs.
"Turkey's warnings should be seen not as meddling in internal affairs, but as the sadness felt by a friend, the shock it experienced and as efforts to draw attention and to help," Gul said.
The Turkish Foreign Ministry said Botsali was returning to Turkey later on Friday. It was not clear when the two ambassadors would return to their posts.
Nationwide marches were called in Egypt after Friday prayers to denounce the security forces' assault. Protests were also planned in Turkey and a pro-Islamic charity group said it would hold funeral prayers in Istanbul for the dead.