"I will never have respect for those who come to power through coups," Erdogan said Saturday.
Egypt's Foreign Ministry said it considered the Turkish envoy "persona non grata" and asked him to leave the country. The ministry said it will scale back its diplomatic relations with Turkey to the level of charge d'affaires.
"This (Turkish) leadership has persisted in its unacceptable and unjustified positions by trying to turn the international community against Egyptian interests and ... by making statements that can only be described as an offense to the popular will," the Foreign Ministry statement said.
A Turkish ministry statement said Egypt's interim government, "which came to power in exceptional circumstances," was responsible for the deteriorating relations.
"The deep-rooted ties and bonds of brotherhood between the people of Turkey and Egypt will remain," the statement said. "We hope that stability and democracy in Egypt is restored as soon as possible and that relations between the two countries are normalized."
Turkish President Abdullah Gul told reporters that he hoped the two country's relations "will be restored soon." Turkish Foreign Minister Ahmet Davutoglu said he believed ties would be restored "once a government elected by the will of the people" comes to power in Egypt.
Since Egypt's 2011 uprising against Morsi's predecessor, autocrat Hosni Mubarak, Turkey sought to strengthen ties with the country's new political order. The Turkish president was the first to visit Egypt after the fall of Mubarak in February 2011. Trade between the two countries increased by about 27 percent in the following year to $3.8 billion in the first nine months of 2012. Turkey also increased its investment in Egypt and currently has some 26 development projects in Egypt.
Turkey's Islamic-rooted ruling party strongly backed toppled Egyptian President Mohammed Morsi a leading figure in Egypt's Muslim Brotherhood as an example for the Arab world of a democratically elected Islamist leader. Turkey criticized his popularly backed July 3 overthrow by Egypt's military, while also criticizing the West for what it deemed as a weak response to the coup.
Turkey and Egypt previously recalled their ambassadors in August after Turkey condemned the ouster and a subsequent bloody crackdown on pro-Morsi protests. Turkey's ambassador returned weeks later, but Egypt declined to return its envoy to Ankara.
Saturday's decision comes after Erdogan renewed his criticism of Egypt's new leaders, dismissing the trial of Morsi on charges of inciting murder of his opponents while in office and describing the situation in Egypt as a "humanitarian drama." He had previously called for the trial of Egypt's new leaders for the crackdown.
At a speech Saturday, Erdogan made the four-finger gesture that refers to a sit-in near a mosque in Cairo where a bloody security crackdown killed hundreds of Morsi supporters in a show of solidarity with Islamists.
Egypt's interim President Adly Mansour has said that Turkey should have relations with "Egypt and its people and not with leaders of a certain group."
Egyptian officials and media have repeatedly accused Muslim Brotherhood leaders of meeting in Turkey to plan protests and other ways to undermine the new government in Cairo.
On Saturday, the independent Egyptian daily newspaper al-Watan reported on its front page that the international members of the Muslim Brotherhood continued "their plotting" against Egypt in a meeting in Istanbul. The paper was referring to a human rights conference in which participants said they will take legal actions against Egypt's new leaders for what it said were "massacres" against supporters of Morsi.
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Frazer reported from Ankara, Turkey. Associated Press writer Desmond Butler in Istanbul contributed to the report.