The June 2 verdicts in the trial of Hosni Mubarak, the former president of Egypt, and senior Interior Ministry aides constitutes a mixed and highly flawed message. Mubarak's conviction in connection with the killing of pro-democracy protesters, along with that of former interior minister Habib al-Adli, affirms that even the highest-ranking state officials are not above the law. But the same three-judge panel acquitted four high-ranking Interior Ministry officials, including those who had direct command of security forces during the January 2011 confrontations that marked the beginning of Egypt's uprising. The failure to determine any direct responsibility on the part of those actually commanding the security forces leaves the Mubarak and Adli convictions open to doubt and reversal on appeal and sheds no light on the operation of the "deep state" machinery of repression.

Mubarak, al-Adli, and the four top Interior Ministry aides were all charged with complicity in murder and attempted murder in connection with the killing of 225 peaceful anti-government demonstrators and wounding of more than 1,800 between January 25 and 31, in 2011. The judges convicted both of knowing about, but failing to prevent, the security force shootings. My colleagues who observed the trial found some procedural flaws, but overall they considered that head judge Ahmad Refaat conducted it in accordance with international fair trial principles. However, the convictions and acquittals alike appeared to reflect serious deficiencies in the case put together by the public prosecutor's office – deficiencies that could also explain the repeated failure to win convictions against more than a few of some 150 high and low-ranking security officers, who have been brought to trial in separate cases around the country in connection with the killing of protesters.

The trial and its aftermath underscore the longstanding problem of impunity in Egypt; a problem that this trial, despite Mubarak's conviction and life sentence, only reinforces. The office of public prosecution is headed by a longtime Mubarak-appointee, Abdel-Meguid Mahmoud. A big part of the impunity problem is that when it does bother to open criminal investigations of police abuse, it often does not secure the evidence needed to convict. This, at least in part, reflects failure by key parts of the security apparatus to cooperate. In the Mubarak trial, the defence counsel - in their closing arguments - contended that while Mubarak and the Interior Ministry officials are being tried for complicity in murder and attempted murder, the prosecution did not identify the people actually believed to be responsible - in its charging documents or elsewhere.

The lead prosecutor in the Mubarak trial, Mustafa Suleiman, told the court on January 4 that the Interior Ministry and the national security section of the General Intelligence Service refused to provide requested documents and evidence; saying that this lack of cooperation was intentional or at least negligent. The GIS is headed by a high-ranking military officer - until January 2011, it was Major General Omar Suleiman. Egypt's ruling junta, the Supreme Council of the Armed Forces, could have instructed the GIS and the Interior Ministry to cooperate with the investigation if it had wished to do so.

Perhaps, the most astounding feature of the Mubarak and Adli verdicts is that the four high-ranking Interior Ministry officials also facing charges got off scot-free. They included the commander of the Central Security Forces and the head of Cairo security. Egyptian rights activists used to spot them frequently on the scene directing security forces during confrontations with demonstrators. The other conclusion one can draw is that Mubarak's conviction and sentencing comes nowhere close to meeting Egyptian demands for comprehensive accountability for systematic abuses under Mubarak's nearly 30-year rule. A survey of a cross-section of Egyptians over the past year found that they care deeply about accountability for human rights abuses.

The serious crimes this trial addressed were limited to those that took place January 25 to 31 - the initial week of the uprising that led to Mubarak's ouster. What is still needed are credible and impartial investigations and prosecutions for torture, enforced disappearances, and other systematic human rights abuse - not to mention serious rights violations, including torture, under the generals who eased Mubarak out of power. Mubarak after all was tried before an ordinary criminal court, subject to ordinary criminal law and procedures, as he should have been. But since he was forced from office in February 2011, some 12,000 civilians have faced military court trials for ordinary crimes as well as protest-related offences.

Joe Stork is deputy director of Human Rights Watch's Middle East and North Africa division