In Parliament, Kemakeza held several ministerial posts. From 1989 through 1993 he was minister of housing and government services and was minister of forests, environment, and conservation in 1995-96. After the 2000 coup he was made deputy prime minister and minister for peace and national reconciliation. It was from this position that he gained the most power. Part of his duties after the Townsville accords was to oversee the distribution of compensation to the victims of ethnic cleansing and to help them reclaim their property. This brought him great visibility and helped to bring him the leadership of the PAP. He was, however, briefly embroiled in controversy over his handling of some of the money set aside for compensation and was dismissed from his post briefly. He maintained he had done nothing wrong and was soon reappointed.