Sudan troops are generally loyal to President Omar al-Bashir
The UN-African Union mission in Sudan is helping Darfur rebels by supplying them with equipment, Sudan's army says.
The military said rebels had stolen six trucks from the peacekeepers, but the UN had failed to report the incident.
The joint UN-AU mission, Unamid, dismissed the accusation, saying the stolen trucks had been reported.
The BBC's James Copnall says the claim highlights the frosty relations between allies of President Omar al-Bashir and the international community.
The International Criminal Court (ICC) is due to rule on Wednesday whether to charge President Bashir with genocide over killings in Darfur.
The court already has a warrant for his arrest on war crimes, but it is due to rule on a prosecution appeal to have genocide charges added.
The court accuses Mr Bashir's government of backing Arab militias who killed thousands of black African Darfuris.
Mr Bashir has repeatedly said he had no control over the actions of people on the ground in Darfur at the height of the violence in 2003 and 2004.
The UN has estimated 300,000 people died in the worst years of the Darfur conflict, and says some 2.5 million are still living in temporary camps. The government disputes these figures, saying they have been exaggerated.
In a statement broadcast on TV in Sudan, the army accused Unamid of colluding with rebels from the Justice and Equality Movement (Jem) - one of the group which took up arms in 2003.
But Unamid spokesman Kemal Saiki told the BBC that he rejected the accusations and insisted that the peacekeeping mission was impartial.
He said Unamid reported the carjacking of the lorries - which belonged to a contractor - the same day it happened.
Unamid has some 20,000 personnel in Sudan.
Sudan's government refused to let the UN run a peacekeeping mission in Darfur on its own and so it is jointly operated with the African Union.
The conflict in Darfur has fizzled out in recent years but no peace deal has been reached.
In 2009, more people were killed in conflict in Southern Sudan than Darfur, the UN says.