The South Sudan rebels now want amendments to the Framework Agreement penned in Khartoum on Tuesday.
The rebel movement's director of information and public relations, Mr Mabior Garang de Mabior, said that they were opposed to the dividing of the country into three regions, the invitation of foreign forces and the resumption of oil production prior to a comprehensive negotiated settlement.
"South Sudan is one country and cannot be divided into three," said Mr de Mabior in reaction to proposals that the country should have three capitals--Juba, Wau and Malakal.
According to a document leaked to the media on Tuesday, the two sides had agreed to a peace deal, including the declaration of ceasefire in the country.
However, rebel leader Riek Machar was later quoted saying that his side needed two days to review the peace deal.
Dr Machar said in Khartoum that they had asked to be given two days more days for consultations among their party and with other opposition factions before signing the deal.
Khartoum peace talks resumed in Khartoum on Monday under Sudanese President Omar Bashir and his Ugandan counterpart Yoweri Museveni.
According to the Framework Agreement, the two rivals agreed, among other things, to allow the Khartoum government to secure the oil fields in South Sudan in coordination with the Juba administration, and to rehabilitate the wells to restore the previous levels of production.
They also declared to work together again for the third time after their long disagreement proved difficult for peace and stability.
President Bashir on Monday promised to end the war in South Sudan and pave the way for rigorous development in the war-torn state.
"I would like to assure everyone that Sudan will work hard and try all measures based on our experience during the war and peace times to ensure that this initiative is a success.
"We shall use our experience in the management of national and community dialogues to address all the issues," President Bashir said.
Interestingly, however, the Sudanese leader is a suspect wanted by the International Criminal Court (ICC) for war crimes and crimes against humanity and genocide committed in western Darfur region.
South Sudan attained independence from Sudan in 2011 but descended into a civil war two years later. The war erupted following a power wrangle between President Salva Kiir and his former deputy Dr Machar.
The war has caused one of the largest humanitarian crises in the continent, according to the UN. About 2 million South Sudanese have become refugees in neighbouring countries.
The International Crisis Group estimates that more than 100,000 lives have been lost in the young nation from from 2013 to 2015 alone.