UPDATE 12:44 GMT
At least two Palestinian worshippers are thought to have been injured. Quds Network tweeted images in which one man can be seen lying on a stretcher with blood on his neck and chest.
The Waqf, the endowment that holds custodianship of Al-Aqsa, confirmed reports of injuries, saying that "several people were lightly injured as a result of clashes," Haaretz reported. The Waqf added that "the [Israeli] police blocked the exits from inside the mosque compound, causing further unrest."
Reports as to the cause of the violence are mixed. Haaretz quoted Israeli police sources as saying "in an unclear and inexplicable step, stones and fireworks were thrown at the police forces."
The heavy handed response by Israeli forces seems to have escalated the situation. Al Jazeera Arabic tweeted a video showing intense firing inside the compound, as Palestinians sought shelter near buildings. Meanwhile, Lebanese newspaper the Daily Star reported that "Israeli police sealed the gates to Jerusalem's flashpoint Al-Aqsa Mosque compound."
Reports have emerged that Israeli occupation forces are shooting rubber-coated steel bullets and tear gas at Palestinian worshippers in Jerusalem's Al-Aqsa mosque compound.
Videos show Palestinians running from approaching Israeli soldiers, as shots can be heard being fired in the background. Smoke can also be seen engulfing the compound, believed to be coming from tear gas canisters fired by Israeli forces to disperse the crowds.
A number of Palestinians have seemingly been arrested and can be seen being escorted through the compound by armed Israeli forces in riot gear. Others shared images from inside the Al-Aqsa Mosque itself, where women and children can be seen sheltering from the violence.
Initial reports added that Israeli forces have chained the gates of the mosque.
The compound, which is situated in Jerusalem's Old City, is the site of Friday prayers for thousands of Palestinians. Today's violence comes just a week after over a thousand Israeli settlers stormed the Al-Aqsa compound under the protection of Israeli occupation forces.