
The verdict follows prolonged legal proceedings, after Egypt’s top appeals court in April ordered a retrial following appeals filed by 16 defendants.
The defendants including Americans, Europeans, Egyptians and other Arabs were handed prison sentences of between one and five years in 2013.
The case stirred heavy criticism of Egypt and raised concerns over restrictions on civil society.
Many of the defendants were tried in absentia and the accused were sentenced but not jailed.
Since 2011, authorities have regularly accused civil society organisations of seeking to destabilise the country.
Egypt stepped up its crackdown on non-governmental organisations after the military ousted Islamist president Mohamed Morsi in 2013.
Morsi’s overthrow was led by general-turned-president Abdel Fattah al-Sisi, who took office in 2014.
Rights groups have accused Sisi’s government of human rights violations and over the repression of dissidents.