Witnesses on the ground in occupied Jerusalem (holy city of Quds) told Al Jazeera that the Israeli police entered the mosque shortly before 7am local time (0400 GMT) on Monday.
Sources told Al Jazeera the officers used the Bab al-Maghariba gate to enter the compound.
They reportedly fought with the worshippers, who have barricaded themselves at the mosque.
Masked Palestinians barricade one of the doors of Jerusalem's al-Aqsa Mosque, one of Islam's holiest sites, on September 27, 2015, as they plan to remain inside to protect it in case of Israeli aggression; @AFP
Al Jazeera's Imtiaz Tyab, reporting from Jerusalem, said clashes continued and tensions "are high" as far-right Jewish groups prepare to enter the mosque compound.
He said several police officers were spotted at the roof of the mosque.
He quoted witnesses as saying that the police fired the stun grenades through windows at a small number of worshippers, and used metal barricades to shield themselves as they approached the mosque's main gate.
For their part, the worshippers threw stones and hurled fire crackers at the police, the witnesses said.
"The confrontations are relatively minor but they are ongoing," Al Jazeera's Tyab said.
The fresh violence occurred on the Jewish holiday of Sukkot, which began on Sunday evening. During the week-long holiday, many Jews visit Jerusalem.
According to a 50-year long agreement, Jews and people of other religions are allowed to enter the compound between 7:30am and 11:30am local time, but are not allowed to pray.
Palestinian worshippers, however, said that far-right Jews have been provoking them by praying, thus violating the agreement.