The Israeli military is gearing for the prospect of a new Palestinian uprising, after violent clashes between security forces and Palestinians in Jerusalem and across the West Bank peaked over the weekend, local media outlets reported on Sunday.

Army Chief of Staff Lt. Gen. Benny Gantz convened a special situation assessment with top brass on Saturday night and instructed to complete preparations for "grave developments," meaning large-scale confrontations that could spark a third intifada, the Yediot Aharonot daily said.

The consultation at the military headquarters in Tel Aviv came hours after some 200 Palestinians and 25 Jewish settlers clashed near the village of Qusra, south of Nablus, over disputed farming land.

Security forces that scrambled to the scene fired stun and tear grenades to disperse the melee. Two Palestinians were reportedly injured by gunfire, one of them severely hurt after a bullet hit him in the stomach. Both the army and settlers claimed that live ammunition was not used during the incident, with one of the latter accusing troops of firing their weapons after running out of non-lethal crowd dispersal means.

Tensions further simmered after Arafat Jaradat, a Palestinian detainee, died at the Megiddo Prison in northern Israel earlier on Saturday from a heart attack. Jaradat, 30, was arrested by the Shin Bet security service just days before his death on suspicion of hurling rocks that two months ago wounded an Israeli civilian near Kiryat Arba, a settlement adjacent to Hebron, Israeli media reported Saturday evening.

Some 3,000 Palestinian security prisoners in Israel jails were expected to launch a hunger strike on Sunday to protest Jaradat's death. Issa Karaka, the minister in charge of Palestinian inmates on behalf of the Palestinian Authority, pinned the blame for Jardat's death on the Israel Prison Service, while the man's family claimed he was in perfect health prior to his incarceration.

Israel's concerns that another intifada is brewing increased after a violent confrontation erupted following Friday prayers at the Temple Mount in Jerusalem. Dozens of Palestinians worshippers began hurling stones and firecrackers at security forces who stormed the compound through the Old City's Mugrhabi Gate and dispersed the rioters with stun grenades.

No injuries were reported in the clash, and police said order was restored within minutes.

However, fiercer clashes erupted in other locations across the West Bank. In Hebron, several dozen Palestinians rallied near the city's Jewish neighborhood to mark 19 years since Israeli settler Baruch Goldstein gunned down 19 Muslim worshippers at the Cave of the Patriarchs in 1994. Protesters threw rocks at security forces on the scene who responded with tear grenades.

Elsewhere in the West Bank, protests were held in solidarity with Palestinians imprisoned in Israel, among them four administrative detainees who have been on hunger strikes for months.

In Ramallah, large police forces deployed in advance to counter Palestinians that rioted at the Bituniyeh checkpoint near the Ofer Prison, firing tear gas and stun grenades at dozens of masked youth.

The military has reported an escalation in violence across the West Bank in recent months, alerting decision-makers to the possibility that Palestinian despair over the gridlock in peacemaking, financial distress and continued settlement expansion could boil to another intifada after years of relative calm.

"Israel and Prime Minister Benjamin Netanyahu will bear the consequences of the intifada that will erupt following the Saturday incident in Qusra," Israeli daily Ma'ariv quoted Palestinian parliamentarian Mustafa Barghouti as saying on Saturday.

Kadorah Fares, head of the Palestinian Prisoner Club, told the paper that the Palestinian public is prepared for a third intifada, noting the death of the Palestinian prisoner on Saturday could possibly light the powder keg.

"All the events point in the clear direction - we are heading towards an intifada," said Fares. "The hunger striking prisoners and the tense demonstrations, the violent incidents in which Palestinian civilians are killed and the political stalemate indicate that we are on the verge of an explosion," he added.

However, senior Palestinian sources in Ramallah assessed the likelihood of another intifada as "slim," according to the Yisrael Hayom daily, which noted that the Palestinians are hinging "great hopes" on U.S. President Barack Obama's visit to the region next month and "his influence" on resuming the peace process.

The newspaper, however, quoted one source as saying that the situation is volatile. "If the worst scenario will materialize - it will be the worst intifada to date," he warned.