[2][4] Most members and resources of Academia Historica were unable to retreat to Taiwan in 1949, and between 1947 and 1951, three presidents of the institution died in office, leading to a suspension of operations due to poor leadership.

In 1957, following the Legislative Yuan's recommendation and under President Chiang Kai-shek's directive, Academia Historica was reopened in Taipei, with construction of archival warehouses beginning in Xindian.

The inclusion of Communist Chinese leaders such as Mao Zedong and Deng Xiaoping as candidates sparked political controversy, which ultimately led to the resignation of Lin Man-houng, the president of the institution.

[6][7][8] On 7 August 2022, Academia Historica's Facebook page published a post referencing a lecture by Hsu Ching-hsiung, former president of the Taiwan Constitutional Law Society, given in the institution's online forum.

[9][10] On 1 August 2016, the institution restricted access to the archives, which were previously fully open, to only citizens of the Republic of China and certain foreign individuals, and introduced a review and appointment system.

[11] On 15 December 2017, DPP legislator Tuan Yi-kang stated that Academia Historica was the most absurd institution of the Republic of China, remarking, "In this age, it is unbelievable that government-led historiography still exists."

[13] On 24 February 2021, Shih Cheng-feng, a professor at National Dong Hwa University, commented that Academia Historica had shown partisan bias under both KMT and DPP administrations, which was a major reason for public distrust.