At the beginning of the second intifada, in the year 2000, the Military Advocate General's Office (MAG's Office) changed its policy regarding Military Police investigations. According to the new policy, the Military Police Investigation Unit (MPIU) would no longer automatically open an investigation into each case in which soldiers killed Palestinians. An investigation would only be opened if soldiers “seriously breached the open-fire regulations and caused physical injury and death.” The new rules stated that, in every case in which soldiers killed a Palestinian, their unit was to carry out an operational inquiry and transfer the findings to the MAG's Office, which would then decide, based largely on these findings, whether to open a Military Police investigation. In cases of abuse, violence, and pillage, in which suspicion arose of criminal behavior by a soldier, the new policy would not apply, and the MAG’s Office would order an investigation upon receipt of the complaint.

In October 2003, B'Tselem and the Association for Civil Rights in Israel petitioned the Israeli High Court of Justice against the new policy. The petitioners requested that the MAG be required to order a Military Police investigation into every case in which a soldier killed a Palestinian civilian who was not taking part in hostilities. In April 2011, in the framework of the petition, the State Attorney's Office submitted a statement to the court indicating that the policy would be changed: a Military Police investigation would be opened automatically in every case in which a soldier killed a Palestinian civilian who was not taking part in hostilities in the West Bank. The policy would not apply to the Gaza Strip.

This policy change is welcome. However, the statement to the court indicates that the decision was made based on the current drop in hostilities in the West Bank, and does not reflect a fundamental change in conception. Should the security situation worsen again, the MAG's office may revert to the policy it held during the second intifada, of not automatically opening an investigation. For this reason, and since the change does not apply to the Gaza Strip, it does not ensure compliance with Israel’s obligations. Therefore, ACRI and B'Tselem did not agree to dismissal of the petition.

The MAG's Office justified the earlier decision to vastly restrict Military Police investigations into death cases by claiming that, since the beginning of the second intifada, an "armed conflict" has been taking place in the Occupied Territories. This, they claimed, released Israel from the obligation to automatically investigate cases of injury to civilians. In its statement to the court, the State Attorney's Office emphasized that the decision to automatically open investigations again did not result from an end to the armed conflict, but rather from the currently calmer security situation. Defining the situation in the Occupied Territories as an armed conflict is imprecise. Some of the military activity in the Occupied Territories is indeed combat actions; however, a significant part of it – such as staffing checkpoints, dispersing demonstrations, arrests – constitutes regular policing, which soldiers carried out during the first intifada, too. Furthermore, international law prohibits intentional attacks on civilians in cases of "armed conflict", too. In every case in which civilians are injured in such a conflict, the incident must be investigated to ensure that the soldiers complied with these rules. Therefore, even under the MAG’s Office’s definition, Israel is not released from its obligation to investigate the killing of civilians not taking part in hostilities by soldiers.

Also, an operational inquiry within the unit of the involved soldier or soldiers cannot properly form the basis for the MAG's decision whether to order an investigation. These inquiries are intended to improve military performance and not to identify persons responsible for violating the law. They are conducted by persons who were directly involved in the incident, who would have to bear the consequences of an investigation, should one be opened. Also, the commanders who conduct operational inquiries are not trained investigators, and cannot carry out a professional investigation on a Military Police level. Testimonies given to B'Tselem by soldiers indicate that, in their units, operational inquiries were carried out negligently and, in many cases, were not carried out at all. One result of the policy not to automatically open investigations until April 2011 was an unmanageable workload for the MAG’s Office throughout the second intifada. Many months would pass, and sometimes more than a year, from the time of the incident to the time that the MAG's Office ordered an investigation. Then, the lengthy delay caused difficulty in locating the victims and eyewitnesses, and made it almost impossible to gather evidence in the field. After investigations were completed, too, long periods of time passed before the MAG’s Office decided whether to pursue legal action. In the vast majority of cases, the MAG’s Office refrained from deciding whether to open an investigation.

Despite repeated requests by B'Tselem, the authorities have not provided the organization with the number of Military Police investigations opened in cases of death during the second intifada. According to B'Tselem’s figures, from 2006 to 2009, soldiers killed 1,510 Palestinians in the West Bank and the Gaza Strip, 617 of whom were not taking part in the hostilities. This figure does not include the 1,389 Palestinians killed in Operation Cast Lead.

B'Tselem has written to the MAG’s Office demanding that a Military Police investigation be opened in cases involving the deaths of 288 Palestinians in 148 different incidents from 2006 to 2009. An investigation was opened only in 22 of these incidents. As of August 2010, the MAG’s Office had reached a decision in only two of the 22 cases investigated; in both cases, the file was closed without any measures taken against the soldiers involved. In the remaining 20 cases investigated, no decision had been reached until then. The MAG's Office informed B'Tselem that an investigation would not be opened in 29 cases, and that 95 other cases were still in process. No information was provided on two cases.

The decision not to open Military Police investigations as a rule, the flaws in operational inquiries, and the negligent handling of the rare investigations that were opened, have all conveyed a message to commanders and soldiers that there is little chance they will be held accountable for injuring innocent persons.