Mohammed Morsi is facing trial on charges of inciting murder and violence
Egypt has told the Turkish ambassador to leave the country and downgraded relations between the two countries.
It follows remarks by Turkish Prime Minister Recep Tayyip Erdogan that Cairo deemed "provocative".
Egypt's foreign ministry said relations with Ankara would be lowered to charge d'affaires, blaming Turkey's continued "interference" in its internal affairs.
Turkey has been a vocal critic of the military overthrow of Islamist President Mohammed Morsi in July.
Mr Morsi, who is in prison awaiting trial, has denounced as illegitimate the court that is trying him on charges of inciting murder and violence.
He is one of thousands of Muslim Brotherhood members that have been detained in a crackdown the interim authorities have portrayed as a struggle against "terrorism".
Hundreds of people have also been killed in clashes with security forces.
Bitter row
Responding to Cairo's decision to expel ambassador Huseyin Avni Botsali, Turkey also announced the downgrading of ties to the level of charge d'affaires.
The foreign ministry also barred Egypt's ambassador to Turkey, declaring him "persona non grata".
The latest deterioration in relations comes a day after Mr Erdogan called for the release of Mr Morsi.
The Turkish leader again condemned the violent dispersal of pro-Morsi protesters in August by Egyptian security forces.
Egyptians have held protests outside the Turkish embassy in Cairo
A bitter row at the time led both countries to recall their ambassadors.
Turkey's ambassador to Cairo returned in September, but the Egyptian ambassador to Turkey was never reinstalled.
Speaking on Saturday, Egypt's Foreign Ministry spokesman said Mr Erdogan's remarks were "provocative and interfering in Egypt's internal affairs".
Turkey is "attempting to influence public opinion against Egyptian interests, supported meetings of organisations that seek to create instability in the country", Badr Abdelatty said.
Mr Erdogan, like Mr Morsi, has his roots in political Islam. Ankara and Istanbul have hosted a series of meetings of the international Muslim Brotherhood.
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