A company of Border Police soldiers have been stationed in Yitzhar following the attack on a military post near the settlement, the IDF spokesman said Friday morning.
The IDF said the decision to have soldiers manning the yeshiva was made according to operational considerations, as it serves as the headquarters out of which violent attacks against nearby Palestinian villages and security forces are launched.
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The yeshiva was evacuated overnight ahead of the military's takeover, and was turned into a Border Police outpost.
The company has been stationed in Yitzhar "in light of the recent acts violence against security forces and in order to meet security demands," the IDF spokesman said.
The army also noted there was a "security necessity to have a constant (military) presence in the settlement."
The IDF spokesman also said that the army and the defense system considers the recent acts of violence and lawlessness to be very grave and will take any measure to put an end to such violence.
"But the more they afflicted them, the more they multiplied and the more they spread abroad (Exodus 1:12)," the yeshiva wrote in response to the IDF's takeover.
"This is the first time the State of Israel closes a place of Torah study, because of the Torah being taught there," the Od Yosef Chai yeshiva said. "Turning the yeshiva's building to a military post is an act of desecration of a holy place, according to the Jewish halacha."
"The yeshiva was previously banished from Joseph's Tomb, but its voice has become louder and louder despite the authorities' constant harassment. In this case as well the yeshiva intends, God willing, to continue Torah study and continue broadcasting the voice of the Torah in the area."
The decision to seize the yeshiva was approved by Defense Minister Moshe Ya'alon, who accepted the IDF's recommendation to take the building using units from the Israeli Border Police.
A security source noted Friday morning that this decision is, "The first step of many decided upon in the meeting that will be carried out in the field in the coming days."
During the situation assessment meeting Ya'alon said, "As far as I'm concerned we're talking about terror and we need to treat these events accordingly. These are intolerable occurrences that are very severe and we must put an end to them."
"To this end we are using a strong hand against these criminals," continued Ya'alon. "We will not ignore violence against soldiers, police, or innocent Palestinians and whoever chooses to behave this way will pay a price."
"We need to take all of the tools at our disposal to deal with this problem, and I don't intend to give up on this issue. If there is responsible leadership in Yitzhar then they need to step forward. If not, we will know to take uncompromising action against this problem as well," said Ya'alon.
Security forces chose to target the yeshiva citing its reputation of extremism. Former commander of the Central Command, Major General Avi Mizrahi, said to Ynet this week that, "This yeshiva doesn't teach Torah. It teaches evil that needs to be eliminated."
The decision is reminiscent of actions taken during the Second Intifada when the IDF took control of Palestinian structures in towns and cities and turned them into permanent outposts manned by soldiers.
The IDF is considering taking further steps against violent settlers including cancelling the yearly pilgrimage to the ruins of the Homesh settlement which takes place every April.
On Thursday, the Jerusalem Magistrate's Court extended the remand of five suspects from Yitzhar settlement who were taken into custody on charges of taking part in the destruction of the nearby military post this week.
At the same time, the courts decided to release two additional suspects, one of whom said, "This is a Bolshevik arrest."
The other released prisoner commented, "We have no connection to this, we're just on a trip in Jerusalem."