"The occupation forces sealed Al Qibli Mosque with steel chains to prevent the Muslims inside the mosque from standing in the way of the colonists' incursions and defending the holy shrine", he said.
Police spokesman Micky Rosenfeld said rocks and other objects were hurled toward police forces Jewish worshippers in a nearby plaza.
Muslims particularly revere the final ten days of Ramadan since they see a sharp increase in visitors who perform I'tikaf (seclusion) and night prayers in Al Aqsa Mosque, the third holiest site in Islam.
The mosque's Palestinian director, Sheikh Omar Kiswani, told Anadolu Agency that 35 Palestinian worshippers had been injured on Monday in clashes with Israeli police - clashes which, he said, had been prompted by the entry into the site by large numbers of Jewish settlers earlier in the day.
He said that the tens of thousands of Muslims going to Al-Aqsa during the month of Ramadan is proof that the Palestinians are sticking by the holy site and the whole city of Jerusalem.
It is located in east Jerusalem, occupied by Israel in 1967 and later annexed in a move never recognised by the global community. He says police forces arrested 16 suspects in the disturbances.
The mosque's social-media team, for its part, shared a video online of police wearing riot gear firing rubber bullets and forcing open the doors of the Al-Aqsa Mosque, in which a number of Palestinian youths were reportedly been hiding.
Netanyahu slammed the language of the draft decision for ignoring Jewish ties to the holy site, and announced that he would be holding an educational seminar for United Nations personnel on Jewish history. Two groups of around 50 Jewish men were said to have shouted racist and provocative slogans and attempted to pray, although it is forbidden for Jews to do so at the site.
Calm later returned to the site, considered sacred to both Jews and Muslims and where clashes regularly occur.
They said Israel and Turkey have reached an agreement to fix ties after six years of strained relations over a deadly Israeli raid on a Turkish ship delivering aid to Gaza in 2010.
Meanwhile, U.N. chief Ban Ki-moon urged Israelis and Palestinians not to allow extremists on either side to fan violence.