Young Palestinians threw stones at Israeli police who deployed at the site, while security forces fired tear gas and sponge-tipped bullets, AFP journalists reported.
Calm later returned to the site, considered sacred to both Jews and Muslims and where clashes regularly occur. A number of injuries were reported by Palestinian media, though the Red Crescent had not provided any figures.
Israeli police spokeswoman Luba Samri said police intervened to allow visits to the site to continue without further incident after "having obtained information on masked youths" taking up positions in the mosque overnight and blocking its doors.
The 10 days, which began yesterday, are the most solemn for Muslims and the period attracts the highest number of worshippers to the site.
Typically non-Muslims, including Jews, are allowed to visit the site during set hours, but cannot pray there to avoid provoking tensions.
The site, known to Jews as the Temple Mount, is located in east Jerusalem, occupied by Israel in 1967 and later annexed in a move never recognised by the international community.
Jordan also denounced what it called "Israeli violations" of rules at the site and said it had been in contact with Israeli officials on the issue.
Similar clashes had broken out yesterday, with the Palestinian Red Crescent saying it took seven Palestinians to an east Jerusalem hospital for treatment of injuries from sponge-tipped bullets, tear gas and beatings.
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