Trouble has flared again despite calls for restraint from the United Nations and the United States, and a warning from Jordan, which has custodianship rights over Muslim holy places in Jerusalem.
The Al-Aqsa mosque site is the third-holiest in Islam, but also revered by Jews as the Temple Mount.
The compound lies in Jerusalem's Old City, an area of great significance to Muslims, Jews and Christians.
The site is also a frequent flashpoint of violence between Jews and Muslims.
The latest violence was triggered over fears Israel is seeking to change rules governing the site which allow Jews to visit but not pray.
Israel's Prime Minister, Binyamin Netanyahu, says the current arrangement will be maintained.
But Chief Palestinian negotiator Saeb Erekat maintains the Israeli government is trying to alter the current arrangement while the world is distracted.
"The plan that the Israeli government is trying to implement, is a horrible and criminal plan that aims to enforce the temporal and spatial division of al-Aqsa Mosque. The Israeli government is taking advantage of how busy the Arabs are with several cases, the world being busy with the international deal of Iran, the world being busy with the refugees going to Europe, and think that they can pass such horrible plans."
Mr Erekat's remarks follow days of clashes between the Israeli police and Palestinian youths, who have reportedly barricaded themselves inside the mosque.
Israeli security forces say they're trying to secure the plaza outside the mosque.
They accused Palestinians of trying to disrupt visits to the compound during the Jewish New Year, which has just ended.
Israeli Police Inspector General Benzi Sau says the timing of the unrest has incited further tension.
"Unfortunately during the last three days we are witnessing attempts by many factors to inflame and to worsen the security situation in the capital, and especially in East Jerusalem to hurt security stability and coexistence."
United Nations Secretary-General Ban Ki-Moon and the United States are voicing concern about the violence at the site.
"The United States remains deeply concerned by the increase in violence and escalating tensions surrounding the Haram al-Sharif/Temple Mount as it's also known. The United States,as we routinely do, strongly condemn all acts of violence particularly at that location that is so sacred to many many people. It is absolutely critical that all sides exercise restraint, refrain from provocative actions and rhetoric,and preserve unchanged the historic status quo on the Haram al-Sharif/Temple Mount both in word and in practice," said White House spokesman Josh Earnest, calling for restraint from both sides.
Mr Netanyahu has held an emergency ministerial meeting, after an Israeli motorist died in a crash police say was caused by suspected Palestinian stone-throwing.
A statement from his office says the Israeli Prime Minister would seek swift legislation to set mandatory minimum penalties for those who endanger human lives by throwing stones, fire-bombs and explosives.
Palestinians fear that increasing visits by Jewish groups to the site, captured by Israel when it seized East Jerusalem and the rest of the West Bank from Jordan in a 1967 war, are eroding Muslim religious control there.
Israel regards all of Jerusalem as its eternal capital, a claim not recognised internationally.
Share
