A statement by the Egyptian Foreign Ministry said Erdogan's speech included "lies and fabrications".
"The Turkish President speech included lies and fabrications and totally disregarded the will of the Egyptian people as reflected in the 30th of June Revolution," said the statement published by local media ONA news and Youm 7.
It said the speech aimed at promoting Erdogan's narrow personal and ideological vision that defies the reality.
"It is not surprising that such fabrication and lies come from the Turkish President, who is keen on creating chaos and spreading division in the Middle East region by supporting terrorist groups and organisations politically, or financially or accommodating them in order to ruin the welfare of region's people, to achieve personal aspirations."
In his speech at the UN General Assembly (UNGA) yesterday, Erdogan had again criticised Sisi.
Erdogan said: "If we are going to defend people who come to power through coups, then I ask the question why we exist as the United Nations."
He said the democratically elected President of Egypt, Islamist president Mohammed Morsi, was overthrown in a coup, and the UN chose to legitimise the person who conducted this coup - a reference to Sisi.
In July, Erdogan described the Egyptian President as a tyrant. Erdogan said that Cairo could not be relied upon to negotiate a truce between Palestine and Israel.
Egypt had expressed deep outrage over Erdogan's comments. The foreign ministry had then said that Erdogan's comments were derived by "personal purpose" and warned that the already sour relations between the two nations could worsen.
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