The Egyptian Foreign Ministry summoned the Qatari ambassador in Cairo on Saturday in light of a statement by his ministry criticizing the Egyptian government.
The Qatari foreign ministry had expressed concern over recent violence and denounced efforts to oppress protests in Egypt.
Seventeen people were killed in confrontations between Muslim Brotherhood supporters and security forces across the country on Friday, the interior ministry said.
"The decision to declare popular political movements as terrorist organizations and describe demonstrations as terrorist acts did not help stop peaceful protests, but paved the ground for shooting protesters with the purpose of killing them," Qatar's foreign ministry said in a statement on Friday.
It added that recent violence in Egypt only proves that security confrontation in Egypt will not lead to stability, suggesting dialogue between the different political factions.
Tension grew between Qatar and Egypt after the army's ouster of Egyptian President Mohamed Mursi in July following mass demonstrations.