Citing a raft of deep systemic failures, human rights group B'Tselem has announced that it will no longer cooperate with Israel's military law enforcement system.

For the past 25 years, B'Tselem, which documents Israeli human rights violations in the occupied Palestinian territories, has served as a "subcontractor" for the system by submitting complaints about soldiers' alleged misconduct, gathering relevant documents and evidence, and requesting updates for affected Palestinian families.

While the goal was to help to bring justice to Palestinian victims and deter future misconduct, the reality has been the opposite, B'Tselem said in a scathing report released on Wednesday.

"B'Tselem's cooperation with the military investigation and enforcement system has not achieved justice, instead lending legitimacy to the occupation regime and aiding to whitewash it," the report noted.

"B'Tselem will no longer play a part in the pretence posed by the military law enforcement system and will no longer refer complaints to it ... The fight for human rights will be better served by denouncing this system and exposing it for what it is."

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The report details a number of cases in which Palestinians have been killed or injured by Israeli soldiers under questionable circumstances, but after a series of apparent investigative failures, no one was held accountable.

In one example, Wadi Samarah, 15, was fatally shot in the back of the neck by an Israeli soldier in the occupied West Bank town of Jenin in September 2007. Samarah, who was targeted as he ran from a group of youths who had been throwing stones at military vehicles, was given no prior warning before the rubber-coated steel bullet was fired towards his head, according to witness accounts.

However, the case was closed for "lack of sufficient evidence" in early 2014, more than six years after Samarah's death.

This case is by no means unique. Since the start of the second Intifada in 2000, B'Tselem has requested investigations into 739 cases in which soldiers killed or injured Palestinians, used them as human shields, or damaged their property.

In 25 percent of these cases, no investigation was ever launched. In nearly half, or 343 cases, an investigation was launched but subsequently closed with no action taken. More than 100 cases are still under processing, but in all of those that have gone through the system, charges were laid in just 25, with another 13 referred for disciplinary action.

These outcomes are the result of incompetent investigations that fail to get at the truth, with few efforts made to collect external evidence or challenge soldiers' statements, B'Tselem said.

"The military law enforcement system is plagued by a host of issues in the basic way it is run: The system is inaccessible to Palestinian complainants, who cannot file complaints with the MPIU [Military Police Investigations Unit] directly and must rely on human rights organisations or attorneys to file the complaints on their behalf," the report found.

"The processing of each complaint lasts months, and even years, so that often enough soldiers who are the subject of the complaint are no longer under military jurisdiction."

Obtaining updates about cases in the system is also fraught with difficulties, as the Military Advocate General Corps operates under a blanket of secrecy, B'Tselem said: "Any attempt to obtain information from them requires repeated communications and in many cases, the information that is ultimately provided is incomplete."

Asked about B'Tselem's announcement, an Israeli army spokesperson maintained that the military justice system is "an independent and professional entity", noting any complaints submitted via this system are probed and, when warranted, an investigation is launched.

"For years the [Israeli army] has been receiving information regarding events which stray from the path of what is expected by [army] personnel ... All information received is examined thoroughly," the spokesperson said, noting the Israeli army would continue to "act as required to enforce the law and maintain the norms" among soldiers.

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The criticisms cited by B'Tselem, however, have been echoed by other organisations, including the Adalah legal centre, which advocates for the rights of Palestinians in Israel and the occupied territories.

"Our experience engaging with Israel's investigatory mechanisms for many years shows that these mechanisms do not comply with the international standards of independence, impartiality, effectiveness, promptness and transparency," Adalah lawyer Nadeem Shehadeh told Al Jazeera.

"As such, the inherently flawed structures of Israel's mechanisms make it nearly impossible to obtain criminal investigations, prosecutions, and punishment of perpetrators of serious violations of international law."

Israel's investigatory mechanisms ... do not comply with the international standards of independence, impartiality, effectiveness, promptness and transparency. Nadeem Shehadeh, Adalah lawyer

Among the key criticisms of Israel's military law enforcement system is its failure to probe the legality or rationale of the directives underlying soldiers' actions, with investigations focusing narrowly on the conduct of implicated soldiers.

In 2014, after Israeli soldiers fatally shot 14-year-old Yusef al-Shawamreh for breaking through Israel's separation fence to access his family's farmland, the case was swiftly closed with no charges laid.

B'Tselem pointed to numerous deficiencies in the investigative process, including a failure to examine the "appalling logic" of the military's apparent plan to lie in ambush for Palestinians breaking through the barrier and to deliberately harm them as a deterrent to others.

On average, in a sample of cases between 2000 and 2011, B'Tselem found that it took four years from the time of the incident to the conclusion of processing the case. In the event that charges are ultimately laid, "this will happen long after the incident, when the witnesses' memory of events has grown dimmer and the evidence has disappeared", impeding the possibility of a fair trial.

The semblance of a functioning justice system allows Israeli officials to deny claims that Israel does not enforce the law on soldiers who harm Palestinians, B'Tselem said, noting it would no longer prop up a system "whose real function is measured by its ability to continue to successfully cover up unlawful acts and protect perpetrators".

B'Tselem spokesperson Sarit Michaeli told Al Jazeera that while Palestinians would still have other options for mediating their cases, this action would help to draw public attention to the system's severe flaws.

"Palestinians will still be able to approach other organisations, or private lawyers, but we will advise people who ask us to do this that we consider it counterproductive," Michaeli said.

Follow Megan O'Toole on Twitter: @megan_otoole