The dispute that began in December escalated into ethnic fighting
South Sudan rebels have denied that they were party to a deal to form a power-sharing government within 45 days to end the conflict.
The rebels' negotiator said they only signed the document that set out how a ceasefire should be implemented at the ceremony in Ethiopia on Monday.
Taban Deng Gai accused the regional mediators of favouring the government side in the political settlement.
Thousands have died and nearly two million fled their homes in the crisis.
The fighting was triggered in December when two factions of the ruling party fell out.
What started as a political dispute between President Salva Kiir and his former deputy Riek Machar has escalated into ethnic violence.
'Violations'Regional mediators presented several documents for the rivals to sign at a ceremony in Ethiopia's capital, Addis Ababa, where peace talks have been going on for months.
But the rebel side, which is loyal to Mr Machar, says it is unhappy that the deal brokered by regional body Igad allows President Kiir to continue in power throughout the proposed two-and-a-half-year transitional period.
Mr Gai said this political document was not signed as his side also objected to the fact that the person who takes the newly created post of prime minister - to be nominated by the rebels - will not be able to run for another political office after the transition.
The BBC's Emmanuel Igunza in Ethiopia says the rebels' move does not come as a surprise.
The rebel faction has been heavily criticised for delaying the peace talks and for numerous violations of the first ceasefire agreement signed in January, he says.
An Igad report has blamed them for all but one violations of the truce.
On Wednesday, the rebels denied an allegation that they shot down a UN helicopter near the oil hub of Bentiu this week.
The UN mission in South Sudan plays a vital role in getting food to the thousands of people who have sought shelter in UN bases around the country.
Up to four million people are at risk of food shortages because of the crisis, aid agencies say.
Fighting erupted in the South Sudan capital, Juba, in December 2013. It followed a political power struggle between President Salva Kiir and his ex-deputy Riek Machar. The squabble has taken on an ethnic dimension as politicians' political bases are often ethnic.
Sudan's arid north is mainly home to Arabic-speaking Muslims. But in South Sudan there is no dominant culture. The Dinkas and the Nuers are the largest of more than 200 ethnic groups, each with its own languages and traditional beliefs, alongside Christianity and Islam.
Both Sudan and the South are reliant on oil revenue, which accounts for 98% of South Sudan's budget. They have fiercely disagreed over how to divide the oil wealth of the former united state - at one time production was shutdown for more than a year. Some 75% of the oil lies in the South but all the pipelines run north.
The two Sudans are very different geographically. The great divide is visible even from space, as this Nasa satellite image shows. The northern states are a blanket of desert, broken only by the fertile Nile corridor. South Sudan is covered by green swathes of grassland, swamps and tropical forest.
After gaining independence in 2011, South Sudan is the world's newest country - and one of its poorest. Figures from 2010 show some 69% of households now have access to clean water - up from 48% in 2006. However, just 2% of households have water on the premises.
Just 29% of children attend primary school in South Sudan - however, this is also an improvement on the 16% recorded in 2006. About 32% of primary-age boys attend, while just 25% of girls do. Overall, 64% of children who begin primary school reach the last grade.
Almost 28% of children under the age of five in South Sudan are moderately or severely underweight. This compares with the 33% recorded in 2006. Unity state has the highest proportion of children suffering malnourishment (46%), while Central Equatoria has the lowest (17%).
Source http://www.bbc.co.uk/news/world-africa-28966971
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