[6][7] Akol was dismissed by Machar in February 1994 and became chairman of one faction of SPLM/A-United following unity with senior SPLA commanders who were under detention by orders of John Garang.

He subsequently signed the Fashoda Peace Agreement with the government in 1997 and was appointed in March 1998 Sudan's Minister of Transportation, a post he held for four years.

In 2002 Akol resigned from the ruling National Congress (NCP), and became a key member of the newly-formed opposition Justice Party.

[5] In 2005 Akol wrote a piece detailing his role as a negotiator on behalf of Garang in the initiation of Operation Lifeline Sudan.

[8] In October 2007, the SPLM withdrew from the Khartoum government; it demanded, among other things, that Akol be removed from his position as Minister of Foreign Affairs, as he was accused of being too close to the regime.