After the end of the civil war in 1991, Tsadkan became general and chief of staff of the Ethiopian National Defence Force (ENDF), leading its rebuilding. He led the reconstruction of the Ethiopian army, but was criticized for lack of ethnic balance when former TPLF commanders formed the core of the force. Under Tsadkan's leadership the ENDF raided an al-Qaeda base in Somalia in 1996, and provided support to rebel forces in Sudan. During the Eritrean–Ethiopian War, he insisted on driving the Ethiopian army into the Eritrean capital of Asmara, but was prevented from doing so by Prime Minister Meles Zenawi. Following the end of the war disagreements within the TPLF led Meles to fire Tsadkan from his position of chief of staff in 2001. Tsadkan later stated that his main issue of dispute with Meles was about lack of democratization in Ethiopia.