Palestinians pray outside entrance to Al-Aqsa in protest against Israeli searches
Sheikh Omar Qiswani, head of the Islamic Waqf, which manages the mosque, told the Muslim worshippers at Lion's Gate not to enter if they have to go through searches.
"We will not receive the Al-Aqsa mosque, except as it was," Qiswani said, rejecting changes made in the aftermath of Friday's shootout, which killed two Israeli police officers and three Palestinians.
The mosque was completely closed for two days after the attack, including the weekly Friday prayers, as were most entrances to the wider Old City area.
In statements ahead of his departure to Paris late Saturday, Prime Minister Benjamin Netanyahu said he had ordered metal detectors installed at the gates as part of new security measures to be introduced at the holy site, also revered by Jews as the Temple Mount.
Palestinians waiting at another entrance to the mosque did enter and police spokesman Micky Rosenfeld said around 200 worshippers had been allowed through for the midday prayers.
"We will also install security cameras on poles outside the Temple Mount [Al-Aqsa compound] but which give almost complete control over what goes on there. I decided that as of tomorrow, in the framework of our policy of maintaining the status-quo, we will gradually open the Temple Mount, but with increased security measures," he said.
Islamic Waqf spokesman Firas Dibs confirmed reports that workers from the Israeli-run Jerusalem municipality had entered the site Sunday morning to clean it before it was reopened – a move they said was unprecedented.
The Waqf said police have confiscated keys to the site and dozens of officers had been stationed outside the main mosque.
Meanwhile, a Palestinian was killed in the West Bank village of Nabi Saleh, and another arrested, after he allegedly opened fire on Israeli forces during an overnight raid Sunday.
An Israeli police statement said 34-year-old Amar Khalil was suspected of carrying out two shootings in the occupied West Bank on Saturday.