After a night of violence in Jerusalem, Israeli police made over 50 arrests and Palestinian medics said 100 were injured during Ramadan clashes in the contested city at the core of the Israeli-Palestinian conflict.

From late Thursday night, police in riot gear and on horseback struggled to keep apart two groups of protesters, with Palestinian youth hurling firecrackers and setting fire to garbage bins and ultra-nationalist Israelis chanting anti-Arab slogans.

The Palestinians clashed with Israeli police amid a dispute over evening gatherings after iftar, breaking the daytime fast during the Muslim holy month.

They said that the police have tried to prevent them from holding their usual Ramadan evening gatherings outside Damascus Gate, a historic landmark on the north side of the Old City and adjacent to several Palestinian neighborhoods.

Meanwhile, hundreds of ultra-nationalist Israelis marched through central Jerusalem towards the Damascus Gate, which police had barricaded as a precaution.

As they marched, many chanted "Death to Arabs," and some waved banners reading: "Death to terrorists."

One participant, David, 40, said he lived far from Jerusalem but "came here to support my own people," adding: "I'm Jewish and I'm a patriot and I'm proud of my country."

Videos were posted on social media purporting to show Palestinian youth assaulting ultra-Orthodox Jews in the city.

Police fired skunk water at the Israelis, pushing them away from their position at the Old City's New Gate, which is just 600 meters away from Palestinians gathered at Damascus Gate.

Police say the measure is part of efforts to ensure Muslims can safely get to the main Islamic prayer site, revered by Muslims as the Noble Sanctuary and by Jews as the Temple Mount.

In a statement in English, Hebrew and Arabic, the U.S. Embassy said it was "deeply concerned" about the violence and urged an end to incitement and a return to calm.

The anti-Arab slogans drew a reproach from far-right Israeli politician Itamar Ben-Gvir, who said he was "against such chants" while defending the Israelis' right to protest.

Clashes and other violent incidents between Palestinians and Israelis have occurred nightly since the start of the Muslim fasting month of Ramadan, on April 13. 

The violence appeared to give way to relative calm by mid-day on Friday, with around 60,000 Muslim worshippers filing past police in the Old City to attend noon prayers at Al-Aqsa Mosque.

But the arrests and injuries raised tensions that spilled over into Friday night and early Saturday, when Palestinian youths again gathered outside the walled Old City and scuffled with hundreds of police in riot gear.

Jerusalem is at the core of the Israeli-Palestian conflict. Israel claims the whole city, including its eastern sector captured in a 1967 war, as its capital. Palestinians seek to make East Jerusalem capital of a future state in the West Bank and Gaza.

Three rockets were fired from the Gaza Strip towards Israel on Friday night, Israel's military said, soon after Gaza's Islamist rulers Hamas and other militants there issued a joint call for Palestinian resistance in Jerusalem.

Two of the rockets exploded near the Israel-Gaza frontier, the military said, and the third was intercepted by Israel's Iron Dome system. There were no reports of injuries.

(With input from Reuters)