Israeli forces have clashed with Palestinians in Jerusalem's Al-Aqsa mosque for the third day running.

The violence on Tuesday morning at the mosque in East Jerusalem was worse than in the previous days, Azzam Khatib, director of endowments and Al-Aqsa Mosque affairs, told Al Jazeera.

The fighting has lasted over Jewish New Year, Rosh Hashanah, after Israeli police raided the site on Sunday "to prevent riots." Al-Aqsa, or Temple Mount as the Jews refer to it, is holy to both Muslims and Jews and has often been a focal point of tension.

Jews are allowed to tour the courtyards of the mosque accompanied by heavily armed Israeli police.

However Palestinian youths had barricaded themselves in to the mosque in order to disrupt the tours over Rosh Hashanah, the police were quoted as saying in Israeli media.

Armed police raided the mosque early on Sunday morning, hoping to open the site as planned and fierce clashes followed.

Palestinians inside Al-Aqsa threw stones and fireworks at the Israeli forces and set up barricades to prevent them from closing the entrance to the mosque, according to Al-Jazeera.

"As the police entered the compound, masked youths fled inside the mosque and threw stones at the force," the Israeli police said in a statement Monday.

The police have now sealed off the compound, preventing Palestinians gaining access to worship, the leader of Mourabitoun movement which guards the mosque said.

The fighting has continued over Rosh Hashanah which lasts until Tuesday night.

Palestinian President Mahmoud Abbas condemned what he called an "attack by the occupier's military and police against the Al-Aqsa mosque and the aggression against the faithful who were there".

East Jerusalem, where Al-Aqsa or Temple Mount is located was seized by Israel during the six-day war in 1967. The international community has never recognised the annexation by Israel and Israel's presence there is considered occupation in Palestinian land.