Under the agreement, both sides promised to free prisoners of war held since the start of sporadic fighting in the country’s western Darfur region in February.
The Darfur rebels are not party to peace negotiations which are currently ongoing in Kenya between the government and the Sudan Peoples Liberation Army.
Africa’s largest country has been engaged in the continent’s longest running civil war, with the oil-rich south seeking independence from the north.
"The government kept its pledge and freed today all 54 detainees from different government prisons," Presidential Affairs Minister Al-Tayeb Ibrahim Mohammed Khair told AFP.
A deal was signed on Wednesday night in Abeche, Chad, following mediation efforts by Chadian President Idriss Deby.
The truce, which came into force on Saturday, is tenuous at best.
Darfur region rebel leader, Mani Arkoi Minawi, told AFP in Cairo that "two government helicopters on Sunday morning bombed one of our bases in an inhabited area of Kutum province."
The SLM has accused Khartoum government of arming Arab tribes in Darfur to stage attacks on non-Arab villages and says it is fighting for an end to marginalization and neglect of the large, impoverished region by central authorities.
Khair said a 15-person committee, made up of five members each from the Khartoum government, the SLM and Chad, would hold its first meeting in the Sudanese border town of Teina, in West Darfur state, on Sunday.