(New York) –The Cairo Appeals Court’s appointment of a civilian judge to investigate the responsibility of three leading former generals for the abuse of protesters is an opportunity to hold military officers accountable for such abuses under military rule. Human Rights Watch has documented the military’s role in detaining and torturing hundreds of protesters as well as the shooting of dozens of protesters under military rule, between January 2011 and August 2012.

Military courts have had sole jurisdiction over any act committed by military personnel and have consistently failed to investigate properly the army’s abuses against protesters, Human Rights Watch said. In the only two cases referred for trial, military prosecutors did not examine senior commanders’ responsibility, including whether they gave orders to commit abuse or failed to prevent crimes by subordinates.

“Over the past year and a half, the military has been getting away with murder, torture, and sexual assault, because military investigators were unwilling to seriously investigate their own,” said Joe Stork , deputy Middle East and North Africa director at Human Rights Watch. “If backed by full support from the political authorities, this civilian investigation could become the first serious step toward reversing the impunity the military has enjoyed so far.”

The civilian investigation comes as a fact-finding committee appointed by President Mohamed Morsy is reviewing abuses against protesters by the military and the police between January 2011 and June 2012. There was little likelihood while the Supreme Council of the Armed Forces was in power that the complaints of military abuse would be seriously investigated, but there is now an opportunity for President Morsy to push for accountability for military abuses in civilian courts, Human Rights Watch said.

On October 15, 2012, the state news agency MENA announced that Samir Abul Muaty, president of the Cairo Appeals Court, appointed Judge Tharwat Hammad as investigative judge to look into complaints filed by private citizens against Field Marshall Hussein Tantawy, former head of the Supreme Council of the Armed Forces and former defense minister, Lieutenant General Sami Anan, former chief of staff, and General Hamdy Badeen, former head of the military police, for their role in violence against protesters during military rule, and for corruption.

On October 16, the Justice Ministry spokesman, Counselor Ahmad Salam, told Reuters that the public prosecutor had received 136 complaints against Tantawy and Anan, which it had referred to Hammad for investigation.

Overall, the military justice system has failed to investigate adequately and prosecute cases involving military abuses such as extrajudicial killings, torture, beatings, and violence against women. The military has not investigated incidents in which video footage captured groups of military police beating and kicking women on December 16, 2011, including one veiled woman who lay on the ground with her torso exposed, while six military police officers beat and kicked her. There has been no investigation of the torture of protesters in March 2011 in downtown Cairo at Lazoghli or in May 2012 at Abbasiyya.

The only cases the military justice system has investigated were the sexual assault of women protesters in March 2011 in a military prison under the guise of “virginity tests”, and the killing by the military of 27 protesters in front of the Maspero building in October 2001. Neither investigation included the responsibility of any senior commanders, however. In the Maspero case, prosecutors refused to investigate the role of the military in the shooting of protesters, but focused only on the crushing of protesters by military vehicles.

The investigations and trials in these two cases underscore the continuing failure of the military justice system to investigate those at senior level even when faced with strong evidence of crimes, Human Rights Watch said. This is hardly surprising, because the military justice system, including the prosecutors and judges, are not independent of those they are investigating, and remain in the same chain of command.

In the killing of 27 Coptic protesters at Maspero in October 2011, only three low-level soldiers were brought to trial by military prosecutors in the killings of 14 protesters. There was no investigation of who commanded the military’s deployment that day, nor of which military officers were responsible for the shootings. On September 3, a military court sentenced the three to prison terms ranging from two to three years for involuntary manslaughter.

On March 11, 2012, a military court acquitted the only military officer charged in connection with the March 2011 “virginity tests” incident. The military prosecutor summoned no witnesses for the prosecution to establish the charges under which he had referred the case to court, nor did he challenge apparently factually inconsistent testimony by defense witnesses. Despite clear statements from senior military leaders conceding that the incident had taken place, the trial did not examine who, and at what rank, ordered the tests.

President Morsy has made public commitments to bring justice to victims of police violence. On July 5, 2012, he established a fact-finding committee to investigate violence against protesters and review the response of state institutions. The committee can make recommendations to the Office of the Public Prosecutor to investigate and prosecute certain incidents, or can present new facts in ongoing investigations.

A lawyer who is a member of the fact-finding committee, Ahmad Ragheb, told Human Rights Watch that the committee agreed to include the “virginity tests” as one of the incidents of violence against protesters it is formally investigating. The committee has until the end of December to prepare a report with recommendations to the president and the prosecution. Despite the fact that military courts have issued harsh sentences, including many death sentences, for crimes committed by civilians, there appears to be a significant discrepancy in sentencing when a military officer is tried, sometimes for the same crime, Human Rights Watch said. In addition to the light sentences in the Maspero case, in February, a military appeals court commuted to three years a five-year prison sentence a trial court had imposed on a military officer found guilty of raping a 34-year-old British woman in a room at a checkpoint in Sinai on May 15, 2011.

Over the past year and a half, Human Rights Watch has repeatedly recommended amending the Code of Military Justice to limit military trials to military personnel and to state explicitly that the (civilian) public prosecutor should investigate complaints regarding abuse of civilians by the military, and to allow officials to try members of the military before civilian courts in cases of abuse and ill-treatment of civilians.

Parliament amended the Code of Military Justice in May 2011, but only to limit the right of the president to refer civilians to military tribunals. The amendments failed to address the broad discretion given to the military in Articles 5 and 7 to try civilians. There was no discussion at the time in parliament about amending the provisions that effectively shield military personnel from trial before civilian courts. As it stands, Article 48 of the Code of Military Justice gives the military prosecution the right to determine whether a case related to military personnel falls within its jurisdiction. In every case, it has insisted on exercising sole jurisdiction over military personnel.

In its long-term work in Mexico and Chile , Human Rights Watch found that having military tribunals deal with human rights abuses committed by military personnel leads to impunity. A 2006 report by the United Nations special rapporteur on violence against women, its causes and consequences, held that after asserting jurisdiction for rapes of women in southern Mexico by the military, “rather than carrying out full and impartial investigations, military investigators have reportedly delayed criminal proceedings and tried to disprove the allegations, thereby placing the burden of proof on the victim.”

“A shift toward a human-rights-respecting culture can only occur in Egypt if it is based on accountability for the most serious abuses of the past year,” Stork said. “Giving the civilian justice system jurisdiction over military abuses committed against civilians is the first step in that direction.”