The annual event comes at a time of particularly high tensions following months of deadly incidents.
The Flag March takes place on Israel’s Jerusalem Day, celebrating its capture of East Jerusalem in the 1967 war.
Israel regards the whole of Jerusalem as its capital, something rejected by most countries and the Palestinians.
The status of the city goes to the heart of the Israel-Palestinian conflict. The Palestinians claim Israeli-occupied East Jerusalem as the capital of a future hoped-for state of their own, though Israel says the city will never be redivided.
There were skirmishes at a flashpoint holy site in the Old City on Sunday morning when Palestinians threw fireworks and rocks at police and towards a gate where Jewish visitors were preparing to enter the grounds, police said. Video showed police firing what appeared to be stun grenades amid reports that masked Palestinians had taken cover inside the Qibli (also known as al-Aqsa) mosque.
The site is known to Muslims as Haram al-Sharif (Noble Sanctuary), and the mosque is the third holiest place in Islam. The same hilltop complex is known to Jews as the Temple Mount and is the holiest place in Judaism.
Last year, a devastating 11-day conflict between Israel and Palestinian militants in Gaza erupted on Jerusalem Day when Gaza’s Hamas rulers fired rockets towards the city after Israeli police and Palestinians clashed at the holy site. On Saturday Hamas called on Palestinians “to rise up on Sunday to defend Jerusalem and the al-Aqsa mosque”.
This year marchers are being allowed to enter the Old City through Damascus Gate which leads into the Muslim Quarter – a decision which was condemned by Palestinians. Last year marchers were not allowed to use this route due to the volatile situation.
Most of the marchers will pass through Damascus Gate, while a smaller number will enter through Jaffa Gate between the Christian and Armenian Quarters, with both converging at the Western Wall in the Jewish Quarter.