At the beginning of the al-Aqsa intifada, the Judge Advocate General's office changed its policy regarding the opening of Military Police investigations for cases in which IDF soldiers kill Palestinian civilians.

In the first intifada, the IDF investigated every case in which a Palestinian was killed except for those in which the person killed was involved in the fighting. When the current intifada began, the JAG's office decided that Military Police investigations would only be opened for those cases in which soldiers "severely violate the open-fire regulations and cause bodily injury or loss of life." Under the new procedure, the army unit investigates every incident in which a soldier from that unit kills a Palestinian civilian. The findings are forwarded to the JAG's office which then decides whether the findings warrant a Military Police investigation.

This change in policy has led to a drastic fall in the number of Military Police investigations. From the beginning of the current intifada (29 September 2000) to 14 February 2007, the Military Police investigated only 239 cases involving shooting by soldiers. Only 30 of these investigations resulted in the filing of indictments. During this period, 3,963 Palestinians were killed, among them 814 minors (under the age of 18). Some of those killed were indeed killed while fighting against Israeli soldiers or civilians, however hundreds of others were not involved in the fighting.

In justifying the change in policy, the JAG's office contends that since the beginning of the al-Aqsa intifada, an "armed conflict" has been taking place in the territories, and that the IDF, therefore, is not automatically required to investigate every attack on civilians. However, it is not correct to define the situation in the Occupied Territories as armed conflict. Some of the actions taking place in the Occupied Territories are indeed combat actions, but a significant number of IDF actions - at checkpoints, in dispersing demonstrations in which the Palestinian side does not open fire, in arresting Palestinians - are normal police actions of the kind that were carried out by soldiers in the first intifada. Furthermore, even if the situation is one of armed conflict, the army is still required to investigate attacks on civilians. Armed conflict, too, has rules, and intentional attacks on the civilian population are forbidden. To ensure that soldiers comply with these rules, such incidents must be investigated.

The JAG's office also contends that the current situation in the territories does not enable the investigation of every case in which a Palestinian civilian is killed. Military Police investigators will undoubtedly face difficulties in conducting their investigations, but these difficulties cannot justify the failure to open an investigation. They can only justify the subsequent closing of the file.

The new procedure is not a suitable alternative to the procedure that was implemented in the previous intifada. First, the new procedure's declaration that only cases of "severe violation" warrant the opening of an investigation is vague and susceptible to various interpretations. The JAG's office did not establish clear criteria for determining when it will request a Military Police investigation. It is no surprise, therefore, that no clear distinction is made between cases in which an investigation is opened and the dozens of similar cases in which the JAG's office decided that an investigation is not warranted. Many investigations were opened only after human rights organizations, diplomats, or journalists put pressure on the JAG's office to do so. The handling by the JAG's office of the death of Khalil al-Mughrabi raises doubts about the manner in which the JAG's office decides whether to open a Military Police investigation.

Second, an internal investigation conducted by a unit cannot properly form the basis for the decision of the JAG's office to open or not open an investigation. At the unit level, the persons directly involved in the incident, and who will bear the consequences of the investigation, are the ones who conduct the investigation. Clearly, this conflict of interest will affect the conduct, as well as the results, of the investigation. Furthermore, the commanding officers conducting the internal investigation do not have the investigative skills of Military Police investigators. Soldiers' testimonies to B'Tselem indicate that the investigations conducted by the units in which they served were carried out negligently, and that in many cases no investigation was conducted at all. The initial decision made by the JAG's office in the matter of the death of Ahmad al-Qureini is a perfect example of the problem of using a unit's investigation to determine whether to open a Military Police investigation.

In addition to the fundamental problems inherent in the new procedure, implementation of the procedure is problematic as well. In most cases, many months (at times more than a year) pass from the time of the incident to the time that the JAG's office decides to open a Military Police investigation. When the investigation is finally opened, the investigators have difficulty in finding the victims and eyewitnesses. Finding evidence at the scene is almost impossible at such a late stage. The problem is aggravated by the fact that the Military Police investigation unit has very few Arabic speakers, and Arabic speakers are needed to take testimonies from witnesses.

The JAG's office relies on these difficulties to explain the small number of investigations and indictments. In some of these cases, though, it has only itself and others in the IDF to blame. The ultimate reason for this failure lies in the improper implementation of the procedure and the flawed manner in which the Military Police investigations are conducted.

The sweeping directive not to open investigations, the flawed handling of the internal investigations by the units, and the negligent handling of the investigations that do occur transmit a message to the commanding officers and soldiers: Even if you breach the rules and harm innocent people, there is little, if any, chance that measures will be taken against you. This message leads to a trigger-happy attitude and to widespread injury and death among civilians in the Occupied Territories.

On 27 October 2003, The Association for Civil Rights in Israel and B'Tselem submitted a petition to the High Court of Justice against the Military Judge Advocate General (JAG). The organizations called on the JAG to open military investigations into all cases in which IDF soldiers kill Palestinian civilians who were not involved in combat. The petition details the circumstances surrounding the death of eight Palestinians who were killed by IDF soldiers between May 2002 and May 2003.

IDF Chief-of-Staff Dan Halutz recently announced a change in the procedure for internal investigations. In a statement to the High Court, the State Attorney's Office called this change a "significant improvement" in the existing situation, an improvement which justifies the rejection of the petition filed by B'Tselem and ACRI.

According to the new procedure, the Judge Advocate General's Office will be provided a detailed report, within 48 hours, of each incident in which a civilian not taking part in hostilities is killed. Based on the information contained in the report, the Judge Advocate General (JAG) will decide whether to open an investigation.

Despite the improvement, the new procedure does not rectify the principal flaws in the process of deciding whether to open an investigation. The responsibility for collecting the information provided to the JAG, which forms the basis for determining whether to open a Military Police investigation, is left in the hands of the military forces that were involved in causing the death. This situation creates a clear conflict of interest in that the persons charged with reporting the primary facts in the case may bear criminal liability for the acts described in the report. Furthermore, the new procedure does not solve the currently existing problem in which the decision to open a Military Police investigation is made long after the incident occurred and the evidence at the scene has disappeared. The request made by B'Tselem and ACRI that the Military Police immediately document the scene of an incident in which a Palestinian civilian is killed so that a future investigation, if ordered, would be effective, was rejected by the State Attorney's Office.

Most importantly, the new procedure leaves intact the general practice of not investigating cases in which civilians who were not taking part in hostilities are killed. This situation transmits a grave message to the soldiers of contempt for the most basic human right, the right to life.

The petitioners have submitted their opinion regarding the new procedure, and the petition is still pending.