Celebrating the capture of all of Arab East Jerusalem 38 years ago, dozens of Israelis entered al-Haram al-Sharif, the home of the al-Aqsa mosque, on Monday in a tour that resulted in scuffles and light injuries.
Hundreds of thousands of Palestinians were forced from their homes in East Jerusalem in 1967 and Palestinians mark the day as al-Naksa (the Setback).
During the day, Aljazeera's correspondent in Jerusalem, Jivara al-Budairi, said thousands of Israelis had flocked to the Old City. The Israeli police put the figure at more than 40,000.
The demonstrators, gathered from across Israel, hoisted Israeli flags and chanted anti-Arab slogans. Members of the Aljazeera crew were also threatened.
Police spokesman Shmuel Ben-Ruby said forces moved in when some of the several hundred Palestinians, who had been praying at the mosque, began throwing stones at the Israeli group.
He confirmed the use of stun grenades.
Director of Palestinian endowments in Jerusalem Adnan al-Husaini told Aljazeera that the Israeli police allowed Jewish extremists to enter the al-Aqsa mosque's courtyard and that he had warned police such a move would provoke a disturbance.
"We have previously warned them not to allow Jewish settlers to enter al-Haram ... especially following Jewish threats last week," he said.
"These extremists carry out their provocative actions, backed by the Israeli police. We no longer expect Israeli police to change their ways."
Security forces told Aljazeera that the visitors were not from the Jewish extremist group Revava that has called for nearly all of the sanctuary to come under rabbinical control.
The site is one of the most politically sensitive in the city. A Palestinian uprising erupted in September 2000 after Israel's opposition leader at the time, Ariel Sharon, toured the compound.
Palestinians want East Jerusalem as the capital of a future state they hope to establish in the Israeli-occupied West Bank and Gaza Strip. Israel regards all of Jerusalem as its capital.