Turkey on Wednesday denounced clashes that erupted inside Israel's flashpoint Al-Aqsa mosque as "unacceptable", saying they violated its "sacred" character.

Israeli police clashed with Palestinians inside Jerusalem's holy site Wednesday, sparking an exchange of rockets and air strikes, in flaring violence as the Jewish Passover overlaps with the Muslim holy month of Ramadan.

"We condemn these attacks," Turkish Foreign Minister Mevlut Cavusoglu said on the margins of a NATO gathering in Brussels.

"Normalisation with Israel has begun, but our commitment cannot be at the expense of the Palestinian cause and our principles," he added, noting that "these attacks have exceeded the limit".

Armed police in riot gear stormed the mosque's prayer hall before dawn, with the goal of dislodging "law-breaking youths and masked agitators" who had barricaded themselves inside following evening prayers.

The Al-Aqsa mosque compound, known to Jews as the Temple Mount, is a site sacred to both Islam and Judaism in the Old City of Israeli-annexed east Jerusalem that has long been a lightning rod in Israeli-Palestinian relations.