At least 13 Palestinians have been wounded when Israeli police fired tear gas and rubber-coated steel bullets at Muslims outside the Al Aqsa Mosque compound.
Israel's decision to remove metal detectors from Al Aqsa Mosque that offended Muslims is "a step in the right direction, but it is not enough," Turkey's President Recep Tayyip Erdogan said on Wednesday.
"Israel is attempting to damage the Islamic character of Jerusalem with new practices every day by taking advantage of the current weakness of Muslims," Erdogan said during an event to discuss higher education in the Islamic world at the presidential complex in Ankara.
"Those who criticise our country whenever possible suddenly become silent when the issue is Palestine, Jerusalem, or Muslims' rights or laws," the president said.
"How sorrowful it is that separations are on the agenda of the Islamic world rather than unity and conflicts, rather than peace."
Anger has spilled across the West Bank since Israel shut Occupied East Jerusalem's Al Aqsa Mosque following a deadly shoot-out July 14.
The site is venerated by Muslims, Christians and Jews.
The mosque was reopened after two days, with Israel installing metal detectors and cameras at its gates.
Three Palestinians were killed on Friday in protests against the measures around the holy site. Three Israelis were also killed in an attack in a settlement in the West Bank.
Israel had initially refused to remove the detectors, claiming the security measures were similar to procedures taken at other holy sites around the world.
But facing a praying protest by Palestinians outside the compound along with international criticism and pressure, Israel's security cabinet decided late Monday to remove the metal detectors.
A statement released after the meeting said a new surveillance system using "smart checks" based on advanced technology would be put in place.
Jerusalem is sacred to Muslims, Jews and Christians – and the Al Aqsa Mosque is the Islamic world's third-holiest site behind the Haram Mosque in Mecca and the Prophet's Mosque in Medina.