Egypt's Foreign Ministry condemned "the storming by Israeli occupation forces of the yard of al-Aqsa Mosque" after prayers at dawn on Sunday.
Clashes broke out between Palestinian youth and Israeli security forces in al-Aqsa Mosque earlier on Sunday, which marks the start of the Israeli new year.
Egypt's Foreign Ministry condemned in a statement what it described as the "attack on the worshippers," who are unarmed Palestinian civilians.
Egypt said it considers the move to be an "unacceptable escalation" against Islamic holy sites "in the occupied Palestinian territories."
Footage of the clashes show sound bombs being fired into the mosque while a small number of worshippers were inside.
Meanwhile, Israeli police spokesman Micky Rosenfeld said on Twitter that police units were in the area in the early morning to "prevent riots by Arabs." He added that two Arabs "involved in stone throwing incidents" were arrested.
Visits to the compound continued regularly afterwards, Rosenfeld said.
Egypt warned from the extreme gravity of continuing the policy of violating religious sanctities, which fuels anger and undermines efforts to resume talks between the Palestinian and Israeli sides.
The al-Aqsa compound in the old city of Jerusalem is a religiously contested site, hosting sacred places of worship for both Muslims and Jews. The division of the area has been one of the most disputed matters in the talks between Palestine and Israel.