The loss of the award - named after Elie Wiesel, a Holocaust survivor and one of the museum's founders - comes as other admirers of Aung San Suu Kyi grow increasingly disillusioned. Mr Wiesel was the first recipient.
An estimated 700,000 Rohingya have fled over the border to Bangladesh since an army crackdown was launched in Rakhine in August.
But Ms Aung San Suu Kyi, the museum said, has failed to live up to that vision.
In response to the museum's action, a spokesman for Suu Kyi said the decision appeared to be based on "the wrong information" and that it made the Myanmar government "very disappointed and sad".
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Since Aug. 25 previous year, over 656,000 Rohingya have crossed from Myanmar's western state of Rakhine into Bangladesh, according to the UN.
"The Government of Myanmar is busy telling the world that it is ready to receive Rohingya returnees, while at the same time its forces are continuing to drive them into Bangladesh", Gilmour said. The military has burned their villages and buried the dead in mass graves.
The UN assistant secretary-general said that during a four-day visit to Bangladesh, refugees told him "credible accounts of continued killings, rape, torture and abductions as well as forced starvation" in the western Myanmar state of Rakhine. In November 2013, we held a public event at the Museum to call attention to our growing concerns, titled: "Our Walls Bear Witness: The Plight of Burma's Rohingya". In private, she becomes angry when the topic comes up, according to people who have spoken with her.
In January, US diplomat Bill Richardson resigned from a Suu Kyi-appointed panel set up to ease tensions with the Rohingya, assailing her for an "absence of moral leadership". It has barred United Nations investigators from Rakhine and has allowed only a few aid organisations to work there. "The conversation now must focus on stopping the violence in Rakhine State, ensuring accountability for the perpetrators, and the need for Myanmar to create conditions for return", Gilmour said.
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Suu Kyi is Myanmar's state counselor and foreign minister. In response, Barack Obama relaxed sanctions, gave financial assistance and became the first sitting U.S. president to visit Myanmar.
For many of her one-time admirers, her handling of the Rohingya issue has been nothing short of a betrayal.
"The ethnic cleansing of Rohingya from Myanmar continues".
In an open letter previous year, Archbishop Desmond Tutu, a fellow Nobel laureate, described her as "a dearly beloved younger sister" whose photograph he had long kept on his desk.
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In an open letter addressed to the Nobel Peace laureate, Director of the museum Sara J. Bloomfield said it was with "great regret" that they were rescinding the award, but it was their duty as a holocaust memorial to stand "in solidarity with victims of genocide and atrocity crimes". They speak Rohingya or Ruaingga, and they have been denied citizenship in Myanmar since 1982.