Muslim worshippers were refused to enter for midday prayers, gathering to pray at an entrance to the compound next to the Lions' Gate entrance gate, following the installation of metal detectors and cameras.
Israel on Sunday reopened the Al-Aqsa Mosque in Jerusalem's Old City with more intensive security measures, following an attack before the holy Friday prayers for Muslims.
Religious authorities protested the installation of metal detectors which Israel says are needed due to "security concerns".
Three gates to the compound still remain closed, Palestinian monitoring groups and activists said.
Worshippers were even refused to enter the mosque for midday prayers.
Dozens of worshippers gathered to pray in front of the Lions' Gate entrance to the compound.
"We reject the changes imposed by the Israeli government," Sheikh Omar Kiswani, the director of Al-Aqsa Mosque, told reporters outside.
"We will not enter through these metal detectors."
TRT World spoke to journalist Gregg Carlstrom in Tel Aviv.
Israeli security forces shot dead a Palestinian in the West Bank town of Nabi Saleh early on Sunday.
Israel's army claims the man allegedly attempted to open fire at them.
The incident comes a day after Israeli forces illegally shut down Islam's third holiest site, the Al-Aqsa Mosque in Jerusalem's Old City, following an attack before the holy Friday prayers for Muslims.
TRT World's Ahmed al Burai discusses the shooting.
A number of Palestinian leaders expressed concerns that Tel Aviv would exploit the attacks to make changes to the status quo on the compound.
Israeli Prime Minister, however, said he told the Palestinian President Mahmoud Abbas that there would be no change to the status quo on the Al-Aqsa Mosque.
Israeli police occasionally restrict Muslim men under a certain age from entering partitions of the site, citing security concerns.
Palestinians argue that Israel's policies towards the compound are aimed at limiting Palestinian presence in the area.
Al -qsa mosque is located in Old City of Jerusalem. It is the third holiest site for Muslims after the Mosque which houses the Kaaba in Mecca and the Mosque of Prophet Muhammad in Medina.
On Saturday, Israel said it would reopen the compound and equip it with metal detectors and cameras.