Activists had hoped that the new African Court for Justice and Human Rights, a merger of two existing judicial mechanisms, would start its work free of political interference.
But leaders and government officials attending an AU summit in Equatorial Guinea last week chose to introduce presidential immunity into the court's rules. The motion was cryptically titled "Protocol on Amendments to the Protocol on the Statute of the African Court of Justice and Human Rights".
It barred the court from prosecuting sitting African leaders and vaguely identified "senior officials".
Netsanet Belay, Amnesty International's research and advocacy director for Africa, said: "At a time when the African continent is struggling to ensure that there is accountability for serious human rights violations and abuses, it is impossible to justify this decision.
"We are deeply disappointed that African heads of state and government have failed to provide the leadership needed to ensure justice for victims of crimes under international law, opting instead to shield themselves and future generations and leaders from prosecution for serious abuses."
Forty-two African and international civil society and rights groups had objected to the amendment, noting in an open letter before the summit that the impunity violated international and domestic laws as well as the AU's own constitution.