On 1 July 1999, the Aboriginal Affairs Commission of the Taiwan Provincial Government was incorporated into the council.

[4] As with all cabinet-level bodies under the Executive Yuan, the Council of Indigenous Peoples is headed by a minister who is recommended by the Premier and appointed by the President.

He was succeeded in 2000 by Yohani Isqaqavut, a long-time indigenous rights activist, chief of general affairs at the Yushan College of Theology, and Presbyterian missionary.

His successor, Chen Chien-nien, had been Taitung County commissioner from 1993 to 2001, a position in which he became known for his dedication to improving the lives of indigenous peoples.

He was accused of buying votes for his daughter, Chen Ying, in the legislative election held three months prior.

Protesters claimed Chang allowed the Atomic Energy Council to dump nuclear waste near indigenous villages, and that the government would not let the Puyuma people participate in its traditional annual hunt without permission from the Forestry Bureau.

[13] Chang was later criticized by several other lawmakers, who questioned her effectiveness in her position, as well as her commitment to securing autonomy for indigenous peoples.

[16] Before the establishment of what was then called the Council of Aboriginal Affairs, there were nine indigenous peoples recognized by the government of Taiwan.

[23] The Council later said that plains indigenous peoples should have registered in the 1950s and 1960s and compared modern Pingpu seeking recognition to "the homeless beggar who kicked out the temple administrator," a Taiwanese analogy used to describe someone who attempts to displace something's rightful owner.

"[27] Despite autonomy being one of the most notable issues among indigenous peoples, many activists feel that the government of Taiwan has not made adequate progress.

[32] The annual exam later began to wane in popularity; in 2009, the proficiency test for the Thao, Saaroa, and Tona Rukai languages had no participants, and the passing rate of test-takers dropped five percent from the previous year.

[33] In 2013, the Council published an online dictionary Archived 12 October 2021 at the Wayback Machine of seven indigenous languages: Bunun, Saisiyat, Tsou, Truku, Thao, Kanakanavu, and Tao.

The Council consulted with tribal elders, speakers of the languages, and linguists to create the dictionary.

[37][38][39] After the enactment of a 2000 law which required the Taiwanese government to either allocate time slots on public television to indigenous culture and education or to create a channel solely devoted to indigenous issues, the council began to push for a channel to be made.

[45] Young indigenous activists criticized the council for a lack of transparency regarding a cross-strait service pact.