Israeli police forcibly evacuated Muslim worshippers from the mosque courtyard before allowing settlers to move through in groups, witnesses say.
More than 1,100 Israeli settlers have forced their way into the flashpoint Al Aqsa Mosque complex in occupied East Jerusalem.
The Jordan-run Islamic Waqf Department, which oversees holy sites in the city, said 1,180 settlers stormed the site and stayed there for more than three hours in a statement on Wednesday.
Ahead of the settler incursion, Israeli police stormed the complex and evacuated worshippers from inside the site, according to eyewitnesses.
Witnesses said dozens of police forces were deployed inside the mosque courtyard before settlers were allowed into the site.
Police forcibly evacuated Muslim worshippers from the mosque courtyard before allowing settlers to move through in groups, they added.
According to witnesses, police used rubber bullets to disperse angry Palestinians, who protested against the settler incursions into the Al Aqsa complex. At least one Palestinian was reportedly injured.
Hundreds of Israeli settlers have stormed the flashpoint compound since Sunday under heavy police protection to celebrate the week-long Jewish Passover holiday.
The Israeli police, meanwhile, imposed restrictions on the entry of Palestinian youths to Al Aqsa Mosque to perform the dawn prayer.
Tension has mounted across the Palestinian territories since last week when Israeli forces raided the Al Aqsa Mosque courtyards, in which hundreds of worshippers were injured.
Daily settler incursions into the flashpoint site to celebrate the Passover holiday have further inflamed the situation.
Al Aqsa Mosque is the world's third-holiest site for Muslims. Jews call the area the "Temple Mount," claiming it was the site of two Jewish temples in ancient times.
Since 2003, Israel has allowed settlers into the compound almost daily.
Israel occupied East Jerusalem, where Al Aqsa is located, during the 1967 war. It annexed the entire city in 1980, in a move never recognised by the international community.