The politician and Nobel peace prize winner received the honour in 2009, when she was living under house arrest.
The rights group said it was profoundly dismayed at her failure to speak out for the Rohingya minority, some 700,000 of whom have fled a military crackdown.
This is the latest honour in a string of awards Ms Suu Kyi, 73, has lost.
"We are profoundly dismayed that you no longer represent a symbol of hope, courage, and the undying defence of human rights," Amnesty's Secretary General Kumi Naidoo wrote in a letter to the Myanmar leader.
"[Her] denial of the gravity and scale of the atrocities [against the Rohingya] means there is little prospect of the situation improving," Mr Naidoo said.
The organisation, which once feted her as a beacon for democracy, announced its decision on the eighth anniversary of Ms Suu Kyi's release from house arrest.