Israeli police have closed the entrances to the top of the Temple Mount after a firebomb was reportedly thrown at a police station.
A blaze broke out at the holy site, Haaretz reported, as all members of the public were evacuated. At least one entrance to Jerusalem’s Old City has also been blocked.
Three people were arrested, police said, amid clashes between police officers and worshippers.
Palestinian media reports suggested members of the Jerusalem Islamic Waqf — the custodians of the site — were involved in the confrontations with Israeli polics, in which at least two Palestinians were injured.
There were also unverified reports of Israeli police entering the Dome of the Rock.
After the sanctuaries were temporarily closed, several dozen worshippers gathered just outside the compound for impromptu prayers, as Israeli police stood watch.
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The site, known to Muslims as the Noble Sanctuary, has been the scene of stand-offs in recent weeks, since an area known as the Gate of Mercy was reopened to Muslim worshippers for the first time since 2003.
Footage circulated through Arab social media sites in recent days showed Israeli forces refusing to remove their shoes in the Bab al-Rahma building and trampling prayer rugs, further exacerbating tensions between Israelis and Arabs.