Lowitja was a chairperson of the National Aboriginal Congress for a short time in the early 1980s. She was later appointed chairperson of the Aboriginal Development Commission. In 1990, she was appointed chairperson of the newly created Aboriginal and Torres Strait Islander Commission (ATSIC). In 1991, she, along with Alf Bamblett and Steve Gordon, became the first Aboriginal people to attend a Cabinet meeting. In December 1992, she became the first Aboriginal Australian to address the United Nations General Assembly. She remained as chairperson of ATSIC until 1996. She was replaced by Gatjil Djerrkura, who was considered by the Howard Government to be more moderate.