The status of Al-Aqsa, known to Jews as the Temple Mount, is one of the most sensitive issues in the Israeli-Palestinian conflict.
Jerusalem: Israeli police said on Sunday that they had detained and were questioning the Palestinian minister for Jerusalem affairs, while a source close to the official said he was arrested in his home.
Palestinian minister for Jerusalem affairs Fadi al-Hadami was detained and was being questioned for "activities in Jerusalem", Israeli police spokesman Micky Rosenfeld told AFP.
Hadami's arrest was most likely due to recent activities that have included accompanying Chile's president during a visit to Jerusalem's Al-Aqsa mosque complex, a source close to the minister told AFP.
On Tuesday, Hadami was seen alongside Chilean President Sebastian Pinera on a tour of the flashpoint holy site, enraging Israel, which said it constituted a violation of regulations and a breach of understandings reached with Santiago for the head of state's visit.
The status of Al-Aqsa, known to Jews as the Temple Mount and located above the Western Wall, is one of the most sensitive issues in the Israeli-Palestinian conflict.
It is the holiest site in Judaism and the third holiest for Muslims after Mecca and Medina, administered by the Muslim Waqf but secured by Israeli police.
Chile later said Pinera's visit was private, with Hadami's presence not part of official protocol. The arrest follows days of violent unrest in Jerusalem.
Overnight Saturday, Israeli police "continued dealing with riots and disturbances in a number of neighbourhoods when stones were thrown at officers and fireworks fired at them," Rosenfeld said in a statement.
Two officers were wounded and six suspects arrested, Rosenfeld said. The continued unrest follows the shooting of a 20-year-old Palestinian in the east Jerusalem neighbourhood of Issawiya by Israeli police, after he had allegedly thrown fireworks at them.
The young man, identified as Mohammed Obeid, died of his wounds, according to the Palestinian health ministry. Israel occupied east Jerusalem and the West Bank in the 1967 Six-Day War.
It later annexed east Jerusalem in a move never recognised by the international community. Israel sees all of Jerusalem as its undivided capital, while the Palestinians see east Jerusalem as the capital of their future state.