The Commission has written to the Egyptian authorities demanding they stay the executions pending further hearings.
It has also asked the authorities to answer charges that the trial which convicted the men and sentenced them in two short hearings was a “complete sham” and the sentences “collective punishment” and “completely arbitrary”.
According to its findings, shown to The Telegraph, the Commission found a “prima facie violation” of the African Charter of Human Rights, of which Egypt is a signatory. In doing so, it agreed to hear arguments for both sides.
The Freedom and Justice Party, the political wing of the Muslim Brotherhood, has taken up the case of the 529, who are accused of being part of a mob that rampaged through a town in Upper Egypt after protest sit-ins against the removal of Mr Morsi were violently cleared with hundreds of deaths.
In the melee, repeated in towns across Upper Egypt, Christian churches were stormed and burned along with public buildings, and a police officer was beaten to death in a hospital.
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However, the case against the 529 was widely criticised after the judge announced at the first hearing he was going to give a verdict at the next session, apparently in response to a lawyer questioning whether the hearing was constitutional.
At the next session, without hearing any evidence, he sentenced all the defendants, most of whom were not in court, to death.
Relatives of some of those sentenced say they were not even in the town on the day in question. Three are believed to be dead.
In a hearing at the court in Minya on Monday, the view of Egypt’s Grand Mufti, which must be given before a death sentence can be confirmed, will be read out. Verdicts are also due on another 628 alleged rioters.
Lawyers in London, where much of the Brotherhood’s remaining leadership is now based after most of its Guidance Council was arrested and detained in Egypt, presented the case to the African Commission, which screens cases to the African Court of Human Rights, earlier this month.
The body is newer and less respected than the European Court on which it is modelled. But it is run by the African Union, which suspended Egypt’s membership following the coup, a decision the country is keen to reverse.
The case was presented by some of Britain’s best-known human rights lawyers, including Michael Mansfield QC, and Lord Macdonald QC, the former director of public prosecutions.
A spokesman for the Egyptian government pointed out that the case against the 529 still had to go to appeal. Only after the full case was complete can it be referred to the president, who has the right to issue a notice of clemency or pardon.
“We have full independence of the judiciary,” he said.