Several police were also get injured in the incident, Palestinians threw stones and fireworks while police were reported to have used stun grenades and tear gas against Palestinians.
According to sources, Police entered the mosque, which is the third holiest site in Islam, after receiving reports that Palestinians had obstructed themselves inside armed with rocks and firebombs.
Police said they went a few yards into the mosque to shut the doors in a bid to restore calm and lock in rebels who were inside and about 300 security personnel had entered the compound when the clashes began.
It was the first time Israeli security forces had entered the mosque since November, when clashes with worshippers also erupted.
The site of the mosque, known as the “Noble Asylum” by Muslims and the “Temple Mount” by Jews, is a holy site for both religions.
The Palestinian government said Israel’s actions proved it wanted to “drag the region into a religious war”.
Police said Palestinian youths had prepared to clash with them, spending the night in the mosque in which they had stored stones and fireworks, as well as wooden planks to prevent police from closing the doors.
Palestinians were angered by what they considered impositions by Jews. Visits are allowed, but Jewish prayer at the site is prohibited.
After Israeli police entered the mosque in November, Jordan one of the very few Arab states with diplomatic relations with Israel recalled its ambassador for three months.
Israel seized east Jerusalem in the 1967 Six-Day War and later annexed it in a move never recognized by the international community.
Israel considers all of Jerusalem as its indivisible capital, but the Palestinians claim the eastern sector as capital of their promised state.
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