Jordan, which has custodianship of Moslem and Christian sites in Jerusalem, said Israel should respect worshippers and international law safeguarding Arab rights.
East Jerusalem tensions have spilled over into clashes between Israeli police and Palestinians around al Aqsa, Islam's third-holiest mosque, at the height of the Ramadan fasting month.
"What the Israeli police and special forces are doing, from violations against the mosque to attacks on worshippers, is barbaric (behavior) that is rejected and condemned," the government said in a statement.
Frictions have mounted in Jerusalem and the occupied West Bank, with nightly clashes in East Jerusalem's Sheikh Jarrah - a neighborhood where numerous Palestinian families face eviction.
Jordanian Foreign Minister Ayman Safadi said the kingdom, which lost East Jerusalem and the West Bank in the 1967 Arab-Israeli war, would do its utmost to protect rights of Palestinians against ownership claims by Jewish settlers.
"Israel as the occupying force carries responsibility for protecting rights of Palestinians in their homes," Safadi said in comments on state media.
Jordan had earlier provided the Palestinians with land deeds in Sheikh Jarrah it says proves Israeli settler claims to the property were groundless.
"The eviction of Palestinians of Sheikh Jarrah from their homes is a war crime," Safadi said.