Right-wing Israelis demonstrate at the Western wall plaza next to al-Aqsa mosque compound, Islam's third holiest site, but also the most sacred spot for Jews who refer to it as the Temple Mount because it once housed two Jewish temples, in the old city of Jerusalem. PHOTO: AFP
Government spokesman Mohammed Momani also said his country, which has custodian rights over the holy site, was examining legal and diplomatic means to protect religious sites in the Holy City.
"Incursions by Israeli forces in Al-Aqsa mosque... and repeated violence against the faithful are a flagrant aggression against Arab and Muslim nations," Momani said.
Israel must "stop these provocations immediately", he said.
Amman is "closely examining legal and diplomatic means aimed at protecting the holy sites against Israeli attacks", he added without elaborating.
Palestinian and Israeli security forces clashed for the third consecutive day Tuesday at Al-Aqsa mosque compound, as Jews celebrated their new year.
The Jordanian-run Waqf organisation which administers the site said Israeli police entered deep inside the mosque and caused damage.
Israeli police said they cleared debris from the entrance and closed the doors on demonstrators who had gathered inside and who had been throwing stones, fireworks and other objects at security forces.
Read: EU warns against 'provocation' at Al Aqsa mosque
The site is the third-holiest in Islam but also venerated by Jews as the Temple Mount.
The protesters fear Israel is seeking to change the rules governing the site which allow Jews to visit but not pray, although Prime Minister Benjamin Netanyahu has said the status quo will be preserved.
On Monday, Jordan's King Abdullah II warned Israel that further "provocation" in Jerusalem would damage ties between the two countries, which have been bound by a peace treaty since 1994.
Read: Clashes rock Jerusalem mosque compound for third day
"Jordan will not have a choice but to take actions, unfortunately," he told journalists after talks with visiting British Prime Minister David Cameron.
Abdullah also discussed Israeli's "aggression" on Tuesday separately with Palestinian leader Mahmud Abbas and Egyptian President Abdel Fattah al-Sisi.
Egypt is the only other Arab country to have a peace treaty with Israel.
Abdullah also called on the international community to take a "firm position" towards Israel and stop its "violations" in a telephone conversation with European Parliament president Martin Schulz.
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