The order to overturn the changes comes less than two weeks since the China-sceptic Democratic Progressive Party was sworn in, replacing the Beijing-friendly Kuomintang (KMT) government.
Outgoing president Ma Ying-jeou oversaw an unprecedented rapprochement with Beijing -- while new president Tsai Ing-wen has said she will maintain the "status quo" with China.
Ties have rapidly cooled since she won the presidency in January vowing to restore Taiwanese pride.
Education ministry officials said the decision on the curriculum, made late yesterday, had been taken in response to public sentiment.
Taiwan split from China in 1949 after a civil war and is self-ruling, but Beijing still sees the island as part of its territory awaiting reunification -- by force if necessary.
Arrests of the protesting students sparked demonstrations across the island, stoked by the suicide of one young activist.
At least 100 protesters were camped out at the ministry for six days.
Deputy education minister Lin Teng-chiao told AFP today the panel that had made the original changes was "not representative" of the island and the procedure was "not proper".
Curriculum changes disputed by protesters included a reference to Taiwan being "recovered by China" instead of "given to China" after the end of Japanese occupation in 1945.
The 50-year period of Japanese rule is also referred to as an era when "Japan occupied" the island, replacing the previous phrase "Japan governed".
"We're glad to see the outcome, which could not have been possible without the efforts of many people," leading activist Lin Fei-fan said.
"One person even died for this cause," he said.
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