However following the death of John Garang in a plane crash in July 2005, Nhial refused entreaties to serve in Khartoum and opted to work in the nascent Government of South Sudan (GOSS).

In 2004, rumors soared across Southern Sudan that John Garang was planning to dismiss Salva Kiir as his deputy and replace him with Nhial.

In December 2008, Nhial was appointed Minister of SPLA and Veterans Affairs by President Salva Kiir, replacing Dominic Dim Deng who died in a plane crash on 2 May 2008.

On 26 August 2011, President Salva Kiir Mayardit unveiled his long-awaited cabinet with Nhial appointed as the minister of foreign affairs and international cooperation of the Republic of South Sudan.

In 2020, President Salva Kiir appointed Nhial as minister of presidential affairs in the revitalized government of national unity.