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During IDF operations against terrorist infrastructure in the areas of the Palestinian Authority (“Operation Defensive Wall”), a dispute arose about burial rights. The Palestinian petitioners requested that the IDF be ordered to cease checking and removing the bodies of Palestinians that had been killed during the course of warfare in the Jenin refugee camp, and that the IDF be ordered not to bury those ascertained to be terrorists in the Jordan valley cemetery. Petitioners also requested to acknowledge that the tasks of identifying and removing the bodies were the responsibility of medical teams and the Red Cross, and that the families be allowed to bring their dead to a quick and honorable burial. 

The Supreme Court of Israel held that the government was responsible, under international law, for the location, identification, and burial of the bodies. As such, teams will be assembled for the location, identification and removal of bodies. The government agreed that the Red Cross should participate in these activities and would "positively consider the suggestion" that the Red Crescent also participate, according to the discretion of the Military Commander. Furthermore, it was established that the identification process be completed as quickly as possible, and will ensure the dignity of the dead as well as the security of the forces. At the end of the identification process, the burial stage will begin; the government allowed the Palestinians to do this themselves, as long as they did it in a timely manner and without threatening Israeli security. Also, no differentiation will be made between bodies (e.g. between the bodies of civilians and the bodies of declared terrorists).

During the 1990s, several complaints of unlawful physical interrogation methods by the General Security Service reached the Israeli Supreme Court. In 1999, it assessed the essential question posed in most of these complaints: was the GSS even allowed to conduct interrogations and if so, did their interrogation methods fall within the scope of torture as prohibited by Israeli and international law. The Court answered the first question in the affirmative and deduced from a general provision in Israeli law the GSS’ authority to interrogate. However, the Court also stated that the GSS was not authorised to use most of the interrogation methods presented to the Court. These included long sleep deprivation, shaking suspects, covering suspects’ heads, and having them crouch on their toes for five minutes intervals. The GSS had argued that the ‘necessity’ defense provided sufficient authorisation to use these interrogations, as information obtained from interrogation might prevent terrorist attacks. The Court did not agree, stating that while the necessity defense might be used by an individual investigator during criminal proceedings, it cannot provide authorisation prior to using the prohibited interrogation methods.    

In 2002, two human rights organisations filed a petition against Israel’s policy to eliminate alleged terrorists by targeted killings. Four years later, the Supreme Court provided a judgment. It acknowledged that Israel is engaged in an armed conflict with terrorist organisations and that therefore, the laws of war should apply. Terrorists, the Court reasoned, are neither combatants nor civilians in the legal sense. The Supreme Court therefore qualified the alleged terrorists as ‘non-legal combatants’. This does not mean, however, that killing these non-legal combatants is always legal. Nor is this always illegal. The Court establishes a framework with four conditions which have to be applied on a case-to-case basis to determine the (il)legality of a targeted killing. The Court reasoned that a targeted killing is only legal if the decision to kill is 1) based on reliable evidence, 2) if there are no other choices to alleviate the danger to Israel’s national security, 3) if the attack is followed by a thorough investigation and 4) if harm to innocent bystanders is limited to the absolute minimum.

As part of the operation to erect a wall in the West Bank, Israel constructed a wall around the Alfei Menashe settlement between 2002 and 2003. This wall also circumscribed five Palestinian villages, the residents of which filed a petition to have the wall removed.

The Supreme Court stated that the military commander of the West Bank had the authority to decide on the erection of a fence, but only if this is necessary for security or military considerations. Also, these security or military considerations had to be proportionate to the infringement on the rights of the Palestinians. In this case, the effects of the wall on everyday life of the residents of the Palestinian villages were so severe that alternatives should have been considered. This had not been the case, the Court stated. Therefore, it ordered the respondents to consider alternatives. 

As part of an operation to prevent attacks on Israeli citizens, the IDF Military Commander in the West Bank issued several Orders to allow the IDF to detain groups of people for periods up to 18 days without the possibility to appeal to a judge or to consult legal counsel.

The Supreme Court held that the military commander is allowed to detain persons if they are considered to be dangerous to the security, but that this authority should be balanced against the liberty of the individual. The Military Commander’s orders allowed for detainees to be held for a minimum of 12 days without judicial reviews and this was considered by the Court to be illegal. Also, the Court stated that investigations should start in an earlier phase of detention. However, the Court also stated that the IDF could prohibit a detainee for meeting with his lawyer because of security considerations. All in all, the Court struck down the disputed orders.