"The parties will continue discussions about the arrangement of the NDA's forces and the percentage of representation in the unity government," Yasir Arman, spokesman for the Sudanese People's Liberation Movement (SPLM), told Reuters.
"These issues were not decided in the agreement signed today," he added.
Saturday's deal agreed on procedures for reorganizing Sudan's legislative, executive and judicial institutions to function in a multi-party political system, Arman said, without giving details.
Arman said the two sides would continue discussing the outstanding issues and any further agreement would be added as an annex to Saturday's deal.
The SPLM, which is part of the NDA, signed a separate peace deal with the Sudanese government in January, ending more than two decades of civil war in the south of Africa's largest country.
The deal stipulated the formation of a new national unity government six months after the January deal, but this has been delayed by a month.
The Sudanese government and the NDA signed a tentative agreement in January which paved the way for the discussions on how to divide up the seats in the new government and how to integrate opposition armed forces into the national army.
Ali al-Mirghani, president of the NDA, signed Saturday's agreement. Mirghani is head of the Democratic Unionist Party, the main party in the NDA. First Vice President Ali Osman Mohamed Taha signed for the Sudanese government.
Other NDA members include the Sudanese Communist Party, the Baath Party, the Beja Congress from the east of Sudan, the Sudan Liberation Movement (SLM) from Darfur in the west and an alliance of southern parties independent of the SPLM.
The NDA was a serious challenge to Khartoum in the 1990s, when it launched a military campaign into the east of Sudan from Eritrea. The group's leadership says it still had thousands of fighters under arms.
Darfur peace talks are proceeding slowly in Nigeria with the government and two main rebel groups, one of which is the SLM, considering a draft declaration of principles.