Dozens of settlers threw stones at a commander and his deputy, who was lightly injured, an army spokesman said. They also hurled paint bottles, smashing the windows of Israeli army vehicles and puncturing the vehicles' tires.
Spokesman Yoav Mordechai said the attack happened after rumors spread of an imminent eviction of settlement outposts.
Settlers also staged a protest in a military zone close to the border with Jordan.
The incidents are a sign of escalating tensions between the army and hard-line nationalist settlers, who believe they have a biblical birthright to live wherever they want in the West Bank, land where the Palestinians want to create a state.
"Security forces should be focused on defending citizens and not dealing with such outrageous breaches of the law," Prime Minister Benjamin Netanyahu said. He ordered ministers and senior security officials to draw up an emergency plan to battle such attacks.
"These are criminals, Jewish terrorists who are harming the soldiers who defend them and the security of Israel," Civil Defense Minister Matan Vilnai said.
Defense Minister Ehud Barak said the "violent actions by a group of extremist criminals bear characteristics of terrorism and are unacceptable."
Similar condemnations were also voiced from within the settler community. Rabbi Haim Drukman, a prominent West Bank rabbi and settler leader, told Israel Radio: "It is hard to believe Jews would do this; it is like the acts of terrorists. How could such wild behavior be directed at the army? Is the army our enemy now? What have we come to?"
Some 300,000 Israelis live in the West Bank, which the government calls by its biblical name, Judea and Samaria.