Twelve settlers from Yitzhar and a student at the community's yeshiva were ordered to leave the area on suspicions that they were involved in attacks on Palestinians.
GOC Central Command Avi Mizrahi issued the warrants, which ordered nine of the settlers to stay out of the West Bank, and three merely to leave the community.
The orders, which were backed by Shin Bet recommendations, are valid between three and 12 months.
Early Sunday morning, police and Shin Bet officers entered Yitzhar and handed out the warrants.
This is an unusual act: The last time so many warrants were issued was in October 2006, when GOC Central Command Yair Naveh ordered 19 persons from their homes.
Israel Defense Forces sources said the warrants were an effective tool. "It's like a battalion commander removed from command who has to issue orders by phone," said a senior Central Command officer.
The most prominent person targeted in the warrants is Akiva Hacohen, who lives on a hilltop near Yitzhar. The Shin Bet considers Hacohen, a married father of four, to be one of the main instigators of attacks on Palestinians. He was handed similar warrants in 2009.
Others include Uriah Cohen, who was previously ordered out of the West Bank in 2006, and Eliav Eliyahu, who was removed fro the area in 2009.
Efi Haikin, the yeshiva student, was recently arrested for allegedly torching the car of the Binyamin police chief during the evacuation of the outpost of Alei Ayin.
While the officers were in Itamar on Sunday, a Yitzhar resident was arrested for insulting a Shin Bet officer. He was brought in for questioning on suspicions of insulting a civil servant. He was released on bail.