Jordan recalled its ambassador to Israel on Wednesday and moved to file a UN complaint after police clashed with stone-throwing Palestinians inside the flashpoint Al-Aqsa mosque compound.
Jordanian Foreign Minister Nasser Judeh said Israel's recent actions at the compound were "way beyond the limits".
"These violations are infuriating the emotions and the sensitivity of 1.5 billion Muslims around the world," he said ahead of a meeting with US Secretary of State John Kerry in Paris.
"Calm has to be restored. Israel has to respect the sanctity of the holy sites."
Jordan has initiated a complaint with the UN Security Council against "repeated attacks by Israel against Muslim holy sites," the official Petra news agency reported.
Jerusalem's Al-Aqsa mosque compound, which is holy to both Jews and Muslims, is one of the most sensitive sites in the Middle East.
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It has been the scene of frequent confrontations in recent months, largely triggered by Palestinian fears that Israel was poised to allow Jewish prayer at the site.
The Israeli foreign ministry said in a statement that it "regrets the Jordanian decision, which does not contribute to calming the atmosphere but the opposite."
Jordan, which administered the West Bank including east Jerusalem before Israel seized it in 1967, has responsibility for managing the mosque compound and other holy sites in the city's Israeli-annexed eastern sector.
Jordan's status as custodian is enshrined in its 1994 peace treaty with Israel.
King Abdullah II vowed on Sunday to oppose any Israeli attempt to change the status of Muslim or Christian holy sites in Jerusalem.
Jordan's Islamist opposition, the Muslim Brotherhood, said it would organise a mass protest in Amman on Friday against the situation at the mosque.