Israeli police were seen dragging a worshipper, while another officer appeared to punch a Palestinian man during the confrontation.
Jews can not pray at Temple Mount, and instead pray at the adjoining Western Wall.
Israeli soldiers wounded nine Palestinians and detained four others Wednesday during protests against new Israeli security measures at the Al-Aqsa Mosque that restrict Palestinians on entering.
They called on the faithful "not to enter the mosque through" the detectors.
Sacred to Muslims, Jews, and Christians, Jerusalem is home to the Al-Aqsa Mosque, which for Muslims represents the world's third-holiest site. Proposals to change security measures at the compound have sparked controversy in the past. "The entire Arab world is up in arms".
Israel closed the site for two days following the attack, angering Muslims and Jordan, the site's custodian. "I believe that they will not let Al-Aqsa have the same fate as Al-Khalil Mosque, cave of discretion, prudency, moderation, and peace patriarchs Abraham, Isaac, Jacob, and Joseph", he wrote in reference to the 1994 massacre at the Ibrabimi Msoque in Hebron where 30 Muslim worshippers were killed by a USA -born Jewish terrorist. The officials spoke on condition of anonymity in line with regulations. The Mughrabi Gate entrance for Jews and tourists already had metal detectors in place.
Muslims regard the same hilltop compound as the Noble Sanctuary.
"Indonesia condemns the steps undertaken by Israeli police, who are limiting access to Al-Aqsa Mosque" the statement released by the Ministry of Foreign Affairs said.
The Palestinians fear Israel is trying to retake control of the site by stealth. The police want the metal detectors to stay put. On Monday it opened to visitors.
Jerusalem police commissioner Yoram Halevy said the metal detectors were necessary for the site to reopen.
Erdan told Army Radio that Netanyahu will rule on the issue after he holds the security consultations.
He added: 'When I go shopping on Friday I pass through a detector at the mall. "We see them everywhere they have become a part of our lives".
The meeting comes ahead of Friday prayers when tens of thousands of worshipers are expected to converge on the the flashpoint holy site, sparking fears of bloodshed, a week after the killing of two Israeli officers at the site by three Arab Israelis.