Egypt summoned Iran's envoy in Cairo on Monday to protest Tehran's criticism of deadly clashes between police and Islamist protesters, the foreign ministry said.
The envoy was told to relay "a strongly worded message" to Tehran, Egyptian foreign ministry spokesman Badr Abdelatty told AFP.
The Iranian foreign ministry had expressed its "regret" and "concern" over the deadly clashes that killed at least 17 people on Friday, according to Iranian media.
The two countries severed ties after Iran's Islamic Revolution in 1979 and Egypt's peace deal with Israel that same year, maintaining only low-level foreign missions.
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Ties warmed during the year-long rule of Egypt's Islamist president Mohamed Morsi, who was overthrown by the military in July.
Morsi and his former aides now face trial on several charges, including the betrayal of state secrets to the Iranian Revolutionary Guards during his presidency.
His followers have organised near-daily protests to demand his reinstatement, despite a harsh crackdown that has killed almost 1,000 people in street clashes and seen thousands more imprisoned, including Morsi himself.
Egypt's military-installed leaders have restored the cold status quo with Tehran, and have lashed out at other countries seen as supportive of Morsi.
The foreign ministry summoned Qatar's envoy on Saturday to protest Doha's criticism of the crackdown on Morsi's Muslim Brotherhood movement.