Police used stun grenades to disperse the Palestinians, Micky Rosenfeld told AFP, adding that there was "high tension" ahead of discussions expected in the Israeli parliament later Tuesday of a plan to annex the site, known to Jews as the Temple Mount.
He added that stones thrown by the Palestinians injured two policemen while three protesters were arrested.
"Police remain deployed at the Temple Mount and visits by tourists are continuing," Rosenfeld said.
The Israeli Knesset, or parliament, is due to debate in the evening a bill introduced by MP Moshe Feiglin, a hardline member of Prime Minister Benjamin Netanyahu's Likud party, which envisages the "application of Israeli sovereignty" over the compound.
The Al-Aqsa compound, which lies in Jerusalem's Old City, is a flashpoint because of its significance to both Muslims and Jews.
Sitting above the Western Wall plaza, it houses the Dome of the Rock and Al-Aqsa mosques and is Islam's third-holiest site.
It is also Judaism's holiest place, as it was the site of the first and second Jewish temples.
The site is in Israeli-annexed east Jerusalem but administered by Muslim religious authorities.
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