Major General Al-Abbas Abdul-Rahman was quoted as saying the rebels blocked a road between Mistry and Kanga in West Darfur state and ambushed the soldiers when they moved in to clear the road.
"As a result, six army elements were killed," Abdul-Rahman, official spokesperson for the Sudanese armed forces, said.
The SMC said the army also clashed with about 1 500 rebel troops in the area of Mistry. It said the rebels were defeated and on their retreat, "They were provided with heavy artillery and mortar fire cover from inside the Chadian borders."
Failed to achieve any lasting settlement for Darfur
Sudan and Chad often trade accusations of supporting rebel groups against each other.
The Darfur conflict has killed more than 180 000 people and driven two million from their homes since 2003.
The latest round of intermittent peace negotiations in Abuja, Nigeria, concluded this week.
More than a year of talks have failed to achieve any lasting settlement for Darfur, which the United Nations has called the world's gravest humanitarian crisis.
UN secretary-general Kofi Annan said on Thursday that he is "gravely concerned" by recent reports of banditry, looting and attacks on civilians and humanitarian workers in Darfur.
He praised the Sudanese government for the inclusion in ongoing peace talks of representatives from Darfur's main rebel group, the Sudanese Liberation Movement, and called for the government "to apply to Darfur the same principles that made possible the Comprehensive Peace Agreement."
That agreement, between the government and southern rebels, promised wealth and power sharing to end a two-decade civil war. - Sapa-AP