The dispute that began in December escalated into ethnic fightingSouth 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.
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