Israeli police patrol the Al Aqsa mosque compound in Occupied Jerusalem after clashes erupted on Wednesday. AFP

In a statement, police said they had "arrested and removed over 350 individuals that violently barricaded" themselves inside the mosque in the Old City of annexed east Jerusalem.

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Those arrested included "masked individuals, stone and firework hurlers/throwers, and individuals suspected of desecrating the mosque," it said.

Clashes erupted inside the Al-Aqsa mosque in Jerusalem as Israeli police said they had entered to dislodge "agitators", a move denounced as an "unprecedented crime" by the Palestinian Hamas.

Israeli police arrest a Palestinian woman at the Al Aqsa Mosque compound on Wednesday. AP

Hamas, which rules the Gaza Strip, called on Palestinians in the West Bank "to go en masse to the Al Aqsa mosque to defend it".

Israeli police said they had entered the mosque to dislodge "agitators" who had barricaded themselves inside with fireworks, sticks and stones.

The mosque compound in the Israeli-annexed Old City of east Jerusalem has previously seen clashes and violence between Palestinians and Israelis, particularly during the Muslim fasting month of Ramadan, which draws tens of thousands of worshippers to Al Aqsa.

Israeli police on a state of alert inside the Al Aqsa mosque compound in Jerusalem. AFP

The holy Muslim site is built on top of what Jews call the Temple Mount, Judaism's holiest site.

The fresh violence comes nearly halfway through Ramadan and as Jews prepare to celebrate Passover from Wednesday evening.

Israeli police have released video footage showing what appear to be fireworks explosions inside the mosque and figures throwing rocks.

Another police video shows riot police with shields advancing through the mosque under a barrage of fireworks explosions.

Palestinian medics check the damage in the first-aid room of the Al Aqsa mosque on Wednesday. AFP

The footage then shows a barricaded door and boxes of fireworks on the floor, as well as police escorting at least five people outside with their hands cuffed behind their backs.

Israeli police said they were forced to enter the mosque after "several law-breaking youths and masked agitators" barricaded themselves inside.

"These instigators fortified it, hours after the (last evening) Taraweeh prayer in order to disrupt public order and desecrate the mosque," the police said in a statement.

"After many and prolonged attempts to get them out by talking to no avail, police forces were forced to enter the compound in order to get them out with the intentions to allow the Fajr (dawn) prayer and to prevent a violent disturbance," they added.

Palestinian youth react as they burn tyres during a protest on the streets of Gaza City on Wednesday. AFP

"When the police entered, stones were thrown at them and fireworks were fired from inside the mosque by a large group of agitators," they continued, adding that one officer was injured in the leg by a stone.

Police "detained the rioters", who "caused damage to the mosque and desecrated it", the statement said, without specifying the number of people detained.

After the announcement of the clashes at Al Aqsa, several rockets were fired from the northern Gaza Strip towards Israeli territory, according to AFP journalists and witnesses.

Agence France-Presse