Deadly violence between Israel and the Palestinians flared Friday as a Jewish holy site was torched in the West Bank, prompting a "very concerned" US President Barack Obama to call for calm.

More than two weeks of violence have sparked concerns of a full-scale uprising and Obama called on both Israeli and Palestinian leaders to tamp down inflammatory rhetoric.

The arson attack on Joseph's Tomb in Nablus came as Palestinians called for a "Friday of revolution" against Israel and as clashes along the border with the Gaza Strip saw Israeli fire kill two Palestinians and wound 98.

Another Palestinian died in clashes in Beit Furik near Nablus, while a Palestinian disguised as a news photographer stabbed and wounded a soldier before being shot dead outside a Jewish settlement in the West Bank.

Seven Israelis have been killed and dozens wounded in the violence so far, while 37 Palestinians have died and hundreds more been wounded in clashes.

In the Palestinian uprisings of 1987-1993 and 2000-2005, thousands were killed and many more wounded in near-daily violence.

Israeli security forces have deployed massively in Jerusalem after two weeks of attacks in the city and across Israel.

Palestinian President Mahmud Abbas, under pressure over recent comments that some have labelled incitement, quickly condemned the fire at Joseph's Tomb, which many Jews believe to be the final resting place of the biblical patriarch Joseph.

Muslims believe an Islamic cleric, Sheikh Yussef (Joseph) Dawiqat was buried there two centuries ago.

The shrine is under Palestinian control and off-limits to Israelis except on escorted trips organised by the army.

Video showed what looked like an extensive blaze, and the Israeli army called it "a despicable act" of desecration.

'Reprehensible attack'

Speaking at a news conference in Washington, Obama said "we are very concerned about the outbreak of violence."

"It's important for both (Israeli) Prime Minister (Benjamin) Netanyahu... and President Abbas and other people in positions of power, to try to tamp down rhetoric that may feed violence or anger or misunderstanding," Obama said.

"Over time, the only way that Israel is going to be truly secure, and the only way the Palestinians will be able to meet the aspirations of their people, is if they are two states living side by side in peace and security."

But right now, "everybody needs to focus on making sure that innocent people aren't being killed."

US Secretary of State John Kerry called Netanyahu to discuss "how best to end the recent wave of violence, and to offer US support for efforts to restore calm as soon as possible," a State Department official said.

Netanyahu and Kerry, who is expected to visit the region soon, are planning to meet in Berlin next week, according to US and Israeli officials, although the exact details have yet to be confirmed.

Netanyahu on Thursday reiterated his willingness to meet Abbas, while accusing him of inciting and encouraging violence.

Abbas has called for peaceful protests, but had not explicitly condemned any attacks in the recent wave of unrest until Friday's statement on Joseph's Tomb.

He said the arson "offends our culture and our religion and our morals", and that the damage would be repaired.

Netanyahu has come under immense pressure to halt the violence but the mostly young attackers seem to be acting on their own, with no mastermind for security forces to pursue.

The violence began on October 1, when a suspected cell of the Islamist movement Hamas murdered a Jewish settler couple in the West Bank in front of their children.

Those killings followed repeated clashes at east Jerusalem's Al-Aqsa mosque compound in September between Israeli forces and Palestinian youths.

In New York, UN Secretary General Ban Ki-moon condemned Friday's "reprehensible" attack, at the opening of a Security Council meeting on the violence.