Jordan, which oversees the east Jerusalem mosque, denounced " radical Israeli attempts" to break into the mosque, under the protection of the Israeli army, Xinhua reported.
The kingdom also condemned the arrest of worshippers at the holy site, which is highly regarded in both Judaism and Islam.
On Sunday, Israeli police stormed the al-Aqsa compound, one of the most holy and politically sensitive sites in Jerusalem, forcefully dispersing a protest by Palestinian Muslim worshippers, after Jewish visitors were allowed to visit.
Earlier Monday, Jordan's Minister for Media Affairs said that during the clashes, dozens of Israeli soldiers tried to destroy several windows and doors of the mosque and fired tear gas bombs towards worshippers, resulting in serious injuries to many visitors.
Jordan called for an end to the violence and called on Israel to be accountable for the safety of the mosque and worshippers.
Israeli actions represent a "violation" of international agreements and the peace treaty between Jordan and Jerusalem, the kingdom added.