Following the end of the Gaza Operation in January 2009, the Israel Defense Forces conducted five major "command investigations" in response to complaints and allegations raised regarding IDF's conduct during the Operation. The investigations dealt with five broad areas: allegations of attacks on UN facilities, allegations of attacks on medical facilities and staff, incidents with a large number of civilian casualties, use of munitions containing white phosphorus, and allegations regarding the destruction of private property for military needs. The findings of these investigations are currently being examined by the Military Advocate General in order to determine whether their findings give cause for the opening of criminal investigations by the Military Police. The conclusions and decisions of the Military Advocate General in this regard are subject to the review of Israel's Attorney General and the ultimate review of Israel's Supreme Court. Within the framework of these five broad investigations, 20 specific incidents were examined including four incidents that appear in the Goldstone Report.

In addition to these broad investigations, 80 other incidents have been investigated. Some of these investigations are the result of complaints directly presented to the Military Advocate General or to Israel's Attorney General by Israeli non-governmental organizations including "B'tzelem" and "Adallah". Other investigations were opened based upon reports prepared by international human rights NGO's such as Human Rights Watch and Amnesty International and international organizations such as the International Committee of the Red Cross and the Arab League. Four incidents that appear in the Goldstone report have already appeared in those reports and are currently under investigation within this framework.

Of the more than 100 incidents that have been investigated so far, 15 Military Police criminal investigations were opened almost immediately after their submission, without being referred to preliminary field investigations, since they dealt with suspected acts which were outside the course of operational military activities,  such as the mistreatment of prisoners and theft. One case, thus far, dealing with theft,  has already led, in July 2009, to an indictment and conviction.

All of the findings within the procedures detailed above, including the decision not to open a criminal investigation, are subject to the judicial review of Israel's Supreme Court.

Recently, eight additional criminal investigations by the Military Police were ordered regarding matters more closely connected to "operational activities", including  allegations of shooting towards civilians carrying white flags and directing flechette munitions towards civilians or civilian targets. In total, so far, 23 criminal investigations have been opened. Seven incidents that appear in the Goldstone report are currently under Military Police criminal investigation.

Dozens of incidents, within the 100 cases noted above, have been examined by field level investigations, and based upon these findings decisions are being reached regarding the need to open Military Police investigations. In a typical Military Police investigation, evidence is taken from Palestinian and other complainants who may have witnessed the events. In such cases, the investigative office of the Military Police approaches the complainant to assist in contacting potential witnesses. For example, the investigative office of the Military Police has approached human rights NGO's for assistance regarding currently ongoing cases. Additionally, the investigative office of the Military Police has, via Israel's Ministry of Foreign Affairs, approached the Office of the High Commissioner for Human Rights to receive additional information regarding an incident where claims of use of human shields were raised. That incident remains under investigation.

The State of Israel is fully committed to its obligations under International Humanitarian Law, including the investigation of any credible complaint regarding the violation of the Laws of Armed Conflict.