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More than 37 Palestinians have been injured at Jerusalem's al-Aqsa Mosque, after clashes erupted between Israeli police and worshippers, the Red Cresent said on Thursday.

Thousands of Paletinians took to the streets of Jerusalem on Thursday morning to mark the re-opening of al-Aqsa Mosque, but celebrations were short-lived after Israeli police stormed the holy site.

By the afternoon, police had closed the Bab al-Hatta Gate which leads to al-Aqsa Mosque again, while stun grenades were used against the Palestinian worshippers within the complex.

A group of young Palestinians reacted by throwing stones at the Israeli forces, local media reported.

It comes after Palestinian religious authorities announced an end to a boycott of prayers at al-Aqsa Mosque after Israel agreed to remove metal detectors outside the complex.

The new security checks sparked violence in Jerusalem and elsewhere, including neighbouring Jordan when an Israeli security agent - who later fled the country - killed two Jordanians.

King Abdullah called for Israeli Prime Minister Binyamin Netanyahu to ensure a security guard who killed the two Jordanians at the Israeli embassy in Amman to face trial.

Abdullah urged Netanyahu to "take responsibility and take legal steps including the trial of the killer" according to a royal court statement.