A comprehensive agreement on power sharing was inked by the two sides during the talks, but several major issues including how to divide the seats in the new government and the integration of NDA militants into the national forces were left unresolved.
Nafie said the two sides had agreed to overcome disputes and continue discussing these issues.
The official reiterated that the NDA should take no more than 14 percent of the posts in the new government as specified in a North- South agreement signed between the government and the Sudan People's Liberation Movement, part of the NDA, in January.
On the integration of the NDA's armed forces, Nafie said the two sides confirmed that no forces should be allowed out of the national security apparatuses.
In addition, Nafie said an NDA's delegation is expected to arrive in Khartoum soon to discuss the formation of the new government.
The NDA, an umbrella opposition group, includes a dozen or so largely northern political parties, trade union representatives and the southern rebel SPLM.
The group has been battling both politically and militarily the government of President Omar Hassan al-Bashir ever since he came to power in a military coup in 1989.
The Sudanese government and the NDA signed a tentative agreement in January which paved the way for discussions on the formation of a new government.
According to the agreement, a new government shall be set up six months after the January deal, but this has been delayed due to disputes between the two sides over the government's lineup.