Jordan further condemned the closure of the mosque's gates and restrictions placed on worshippers' entry under any circumstances.
Amman: Jordan's Foreign Ministry on Sunday summoned Israel's ambassador to the country, Amir Weissbrod, in protest over last week's clashes at Jerusalem's Temple Mount compound, when Jewish worshipers were allowed on the site to commemorate Tisha B'Av, which coincided with the Muslim holiday of Eid al-Adha.
Jordan's Foreign Ministry spokesman, Sufyan Qudah, said that the ministry's Secretary-General Zaid al-Lawzi delivered the Israeli ambassador a "decisive letter" to be conveyed immediately to the Israeli government.
In the letter, Jordan voiced its "condemnation and rejection of Israeli violations" at the highly-sensitive site, where Israeli security forces fired tear gas, rubber bullets and sound grenades at Palestinian worshippers last week, Al Jazeera reported.
Jordan supervises the Al-Aqsa Mosque, located in the Old City of Jerusalem, and is considered to be the third holiest site in Islam. The mosque was built on top of the Temple Mount, known as Haram esh-Sharif in Islam.
In the statement, Jordon further condemned the closure of the mosque's gates and restrictions placed on worshippers' entry under any circumstances.
Ayman Safadi, Jordan's foreign minister, tweeted that he met European Union representatives earlier on Sunday to "stress urgency of effective Int'l steps against Israeli's violations of Holy Sites in occupied Jerusalem".
Jordan's diplomatic protest came days after Israeli Minister of Public Security Gilad Erdan reportedly told a radio station that Tel Aviv should work towards allowing Jews to pray at the holy site.
But he added that the change should come through "political agreements and not by force," according to the Israeli newspaper, Haaretz.
However, Jews are only allowed to visit Al-Aqsa Mosque, but they cannot pray there - a ban condemned by some Israeli nationalists, including members of Prime Minister Benjamin Netanyahu's right-wing coalition.
Jordan's foreign ministry expressed "the kingdom's strong condemnation" over Erdan's comments, demanding "an immediate stop to Israel's violations and all its attempts to change the historic and legal status quo" at the site.
The Al-Aqsa Mosque is also a key Palestinian national symbol.
As Muslims around the world marked the Eid al-Adha holiday on August 11, Israeli forces stormed the Al-Aqsa Mosque compound, sparking Palestinian protests.
Eid al-Adha coincided with the Jewish Tisha B'av holiday, resulting in an increase in visits by Jewish worshippers to the holy site.
In a bid to ease tensions, police initially barred Jews from entering, but Muslim worshippers still suspected they would be allowed in and staged protests that sparked clashes.
After relative calm returned and following criticism from Israeli far-right politicians, police reopened the site to Jewish visits, provoking further violence.
The site is located in East Jerusalem, occupied by Israel in the 1967 Six-Day War and later annexed in a move never recognised by the international community.