The announcement of President Thein Sein's action came just hours after hundreds of people demonstrated in Yangon, Myanmar's biggest city, against allowing non-citizens bearing the cards, including many members of the Rohingya ethnic minority, to participate in the referendum.
Most Muslim Rohingya are not citizens, and prejudice against them is high in the predominantly Buddhist nation. Communal tensions have led to violence in recent years which left at least 280 people dead and 140,000 homeless, mostly Muslims confined to squalid camps in the western state of Rakhine.
Thein Sein's move came as a surprise and details remained unclear, along with the reason for the sudden decision. Presidential office director Maj. Zaw Htay said on Facebook that the announcement "automatically annuls the right" of temporary ID card holders to vote.
Parliament had only recently approved the right of the card holders to vote. It had originally opposed it, but reversed itself after an appeal from Thein Sein.
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Those rejecting the measure included the opposition National League for Democracy party of Nobel Peace Prize laureate Aung San Suu Kyi.
However, domestic opposition to the policy appeared strong. Rohingya are generally regarded as illegal immigrants from neighboring Bangladesh, even though many have lived in Myanmar for generations.
The temporary identification cards, popularly called "white cards," were created by the former military regime for the 2010 elections in which it relinquished power to a nominally civilian government, though under heavy army influence. An army-backed political party won seats in areas with sizable numbers of white card holders.