Extremists from ultra-Orthodox settler groups, who say God gave the region to the children of Abraham for all time, have been increasingly active in recent months.
This has taken place as the United States sought to pressure the Israeli government to relinquish the West Bank, or a large portion of it, as part of a peace deal with the Palestinians.
The smoldering crisis escalated sharply Dec. 12 when a mob of angry settlers stormed a regional military base near the Arab city of Qalqilya, stoned the brigade commander and his deputy and burned army trucks.
The right-wing hard-liners attacked the base because, they said, the military was preparing to shut down a settlement the Israeli Supreme Court had ordered closed in August.
Earlier, another group broke into a closed military zone on the border with Jordan and attempted to establish a settlement outpost before they were arrested.
These incidents, with troops under attack from fellow Jews, triggered an outcry in the Israeli media, with some commentators even speculating on "civil war."
The liberal Haaretz daily warned that "the only 'red line' that has yet to be crossed is a scenario in which an Israeli citizen fires on soldiers. There are those in Israel's security forces who fear that day is not so distant."
The violence follows a growing number of so-called price-tag attacks by settlers on Palestinian mosques and churches, some of which were torched. These attacks are intended to dissuade the government from moving against illegal hilltop outposts, a tactic used by the more militant settlers to extend the settlement process.
Ironically, it was one devised in 1997 by Ariel Sharon, then foreign minister in Netanyahu's first term as premier, who exhorted settlers to "seize the hilltops" to prevent the creation of a Palestinian state.
The recent attacks are part of a larger hard-line campaign to prevent the government forcibly evacuating settlements, which the settlers see as a move toward an eventual sellout to the Palestinians.
Israeli Defense Minister Ehud Barak, Strategic Affairs Minister Moshe Yaalon and others branded the attacks as terrorism, an epithet rarely used against Jews and the politically powerful movement representing the 300,000 settlers in the West Bank.
"There's no question that this is terror behavior," declared Barak, Israel's most decorated war hero.
Prime Minister Binyamin Netanyahu, a right-wing hawk widely blamed for undermining the peace process, described the attack on the army as "intolerable."
He directed security forces to be more aggressive against the militants and decreed they would be tried by military courts.
But he stopped short of calling the culprits "terrorists," thus avoiding a politically dangerous clash with the settler bloc by equating the militants' actions with stone-throwing Palestinian "terrorists."
Indeed, the commotion, and the customary condemnations, underlines just how powerless the authorities are when it comes to Jewish terrorism and how success administrations have failed to rein them in.
Even the right-leaning Jerusalem Post was incensed by the attack on the army.
"What needs to be understood is that these settlers and far-right activists largely do not fear the police or the courts," the Post's military affairs correspondent Yaakov Katz, wrote.
"Past experience has shown that punishments tend to be minor and that's in the rare instance where the case actually makes it court."
Palestinians living in the West Bank, who have been under military occupation since 1967, are routinely tried by military courts where defendants' rights are minimal.
Haaretz, which has long spoken out against Jewish terrorism and settler militancy, cited military documents indicating that in 2010 99.74 percent of Palestinians who appeared before military courts were convicted.
That's 25 acquittals out of 9,542 cases.
Despite the government's pledge to crack down of right-wing extremists it has in recent weeks approved settlement expansions in the West Bank and, more controversially, in Arab East Jerusalem where the Israelis have been systematically forcing out the Palestinian population for years.