Israeli police banned last Friday's Muslim prayers at Jerusalem's holiest site after two Israeli policemen were shot dead in a shooting near the site.
The US and the West have said settlement construction and expansion are hindering future plans for a viable Palestinian state.
One of the mufti's bodyguards, Khaled Hamo, said police "entered the crowd and took the mufti".
Israel took the rare step of closing the Temple Mount complex in Jerusalem to Muslim worshipers and tourists through the weekend, after a deadly shoot-out on Friday morning in which three Israeli Arabs killed two Israeli Druze policemen.
He further defended the Israeli decision to close the al-Aqsa Mosque following the Friday incident and said Tel Aviv "has an obligation to make sure that security is maintained".
Qatari Foreign Minister Sheikh Mohammed bin Abdul Rahman al-Thani, who is now visiting the Turkish capital, Ankara, stressed on Twitter his condemnation of the "unprecedented aggression" on al-Aqsa Mosque.
"Metal detectors will be stationed at the entrance gates to Temple Mount and cameras covering activity on the mount will be installed outside it", Netanyahu's statement said. They added they were still working to identify the attackers.
It is the third-holiest site in Islam and the most sacred for Jews.
The three papers said President Mahmoud Abbas had condemned the attack and the closure of the mosque, saying he telephoned Israeli Prime Minister Benjamin Netanyahu to condemn both the attack and the mosque closure.More news: England must respect batting in Test cricket, says Michael Vaughan
Israeli police say a shooting in Jerusalem΄s Old City has caused a number of casualties.
The israeli Arabs are the descendants of Palestinians stayed on their land to the creation of Israel in 1948.
The fighting inside the complex was one of the worst incidents of violence on the Temple Mount in years, and the images of the gun battle and fatalities are liable to raise tensions throughout the region.
It is located in East Jerusalem, occupied by Israel since the 1967 Middle East war.
"The Old City is always off limits on Fridays through 3 p.m. because tensions are always higher and the potential for violence greater", the alert said.
Jordan is a controlling force over the Waqf, the Mount's Islamic custodians.
A wave of unrest that broke out in October 2015 has claimed the lives of at least 281 Palestinians or Arab Israelis, 44 Israelis, two Americans, two Jordanians, an Eritrean, a Sudanese and a Briton, according to an independent estimate.
In September 2000, then-Israeli opposition leader Ariel Sharon made a provocative visit to the site to show Israeli presence, sparking Palestinian protests that quickly escalated into armed clashes between Palestinian gunmen and Israeli soldiers.
"Any Palestinian who resists with any kind of violence risks having [his] home demolished or sealed and [his] entire extended family expelled onto streets".