The IPF is responsible for investigating crimes committed by Israeli civilians against Palestinian residents of the Occupied Territories. The IPF has the duty to accept the complaint, investigate the incident, and collect evidence so that the State Attorney's Office can prosecute. Where the IPF knows from other sources that a criminal offense has been committed, it has the duty to investigate on its own initiative.

In April 1981, a commission, headed by Deputy Attorney General Yehudit Karp, was established in the Ministry of Justice "to ensure, as far as possible, that suspicions about offenses committed by Israelis in the Judea and Samaria Region against Arab residents of that region be investigated speedily, substantively, and efficiently." The Karp Commission monitored some seventy incidents that had been reported at that time, including killings, armed threats, trespassing, assault, property damage, and disturbances of public order. The Commission's conclusions, published in 1984, indicated that the IPF does not act to prevent violations of law and order committed by settlers, and does not thoroughly investigate complaints and suspicions in this area. The Commission determined that the police closed an inordinately high number of files without taking any action, and that the police were lenient with settlers who refused to cooperate when interrogated. In conclusion, the Commission stated that the performance of the IPF is clearly deficient, and that an urgent solution was needed in order to prevent deterioration and the undermining of the foundations of the rule of law.

In 1994 B'Tselem published a report which found serious defects in the IPF's handling of Israeli civilians suspected of committing' offenses against Palestinians in the Occupied Territories. In effect, nothing had changed since the Karp Commission's report was published ten years earlier. In many instances, including fatalities, the IPF did not conduct any investigation. Cases in which no complaint was filed are not investigated, even if the IPF received information of the offense from other sources. In many cases, the IPF was unable to locate the investigation file and, in other cases, the IPF denied that a complaint had been filed, even in cases in which B'Tselem had definitive information that a complaint had been filed. In several cases, files were delayed for a prolonged period after the crime had been solved, with no indictment being filed. Closing of files on grounds of "offender unknown" almost became the norm, despite a number of cases in which identifying details of the offender ostensibly existed.

These deficiencies in police conduct continue today. This situation deters Palestinians from filing complaints because they have a fundamental disbelief in the willingness of the police and the judicial system to enforce the law in cases of violence by Israeli civilians. However, where Palestinians want to file a complaint, police conduct toward them and the manner in which the complaints are handled repeatedly reinforce Palestinian mistrust. Police officers often refuse to accept complaints from Palestinians or send the complainant from one police station to another. During the al-Aqsa intifada, it has been almost impossible to file complaints. This difficulty results from the many restrictions on Palestinian movement in the Occupied Territories, which prevent prospective complainants from reaching the police stations.

The negligence of the IPF in handling crimes imputed to Israeli civilians in the Occupied Territories against Palestinians does not result solely from negligence of investigators or the lack of personnel. The scale, character, and recurrence of the omissions clearly indicate that the failure is systemic and not incidental. The many cases, some involving death, in which no investigation is opened or files have been "lost" suggest that the police are indifferent toward the life, person, and property of Palestinians.