Renewed fighting between Jem, Darfur's main rebel group, and the government broke out in May after the fighters pulled out of peace talks.
The group has protested against the involvement of other rebels in the Qatari-brokered negotiations and has accused the government of breaking an earlier ceasefire.
Jem said on Monday it would continue to boycott the negotiations and was clashing "continuously" with Sudanese army forces in south and central Darfur.
Talks resumed in the Qatari capital, Doha, on Monday, but without the participation of Jem.
Negotiations were instead held between the Sudanese government and the Liberation and Justice Movement (LJM), a rebel group that is an alliance of splinter factions.
Amin Hasan Omar, the chief Sudanese negotiator, said Khartoum was "optimistic" about signing a final agreement with the LJM.
Ahmed bin Abdullah al-Mahmoud, a Qatari mediator and minister of state for foreign affairs, called on other groups to join in the negotiations.
"We hope the negotiations will yield the anticipated results, and [that] the rest of our brothers, without any exceptions, will join," Mahmoud said.
Jem signed signed a framework peace pact with the government in February, a move that was hailed by the international community as a major step toward bringing peace to Darfur.
But there was no final, comprehensive peace agreement by a March 15 deadline and Jem pulled out of the talks that same month, claiming ceasefire violations.
Darfur, a desert region the size of France, has been gripped by a civil war since 2003.
About 300,000 people have been killed in the fighting and another 2.7 million displaced, according to UN figures.
Khartoum says 10,000 people have died.