Sudan's Justice and Equality Movement (Jem) has accused the army of attacks just hours after the rebel group signed a key agreement on Darfur with the government.
Khalil Ibrahim, the Jem leader, said the army attacked two rebel positions.
He and Nafie Ali Nafie, an aide to Omar al-Bashir, the Sudanese president, had emerged from long talks with an agreement on a series of confidence-building measures in the Qatari capital Doha this week.
The deal is supposed to pave the way for broader talks to end the conflict in Sudan's Darfur region.
But Ban Ki-moon, the UN secretary-general, warned both sides that they must renounce violence before a peace deal can be reached.
He described the "goodwill" agreement signed in Doha as "a constructive step" but urged both parties to agree to a ceasefire and attend further "comprehensive and inclusive talks".
"Until the parties renounce hostilities, the situation in Darfur cannot improve," Ban said on Tuesday.
Other rebel factions have refused to talk to Khartoum and Al Jazeera has learnt there are serious disagreements between anti-government groups about the Doha agreement.
Meanwhile, UN officials announced that an international peacekeeping force in Darfur would not reach its target of 80 per cent deployment by March.
|The Jem delegation agreed to 'confidence building measures' with Khartoum [AFP]
More than a year after its deployment, the joint force still operates at around 65 per cent of its capacity.
Eighty per cent of the force was expected to be deployed in March, but the deployment has been postponed by at least three months.
However, Susana Malcorra, the UN undersecretary-general for field support, told the Associated Press that the full 26,000-strong UN-African Union force should be in place by November.
She added that the delay was not linked to an expected decision by the International Criminal Court (ICC) on whether to issue an arrest warrant for al-Bashir on war crimes allegations in the western Darfur region.