A regional official said on Friday that the fighting took place even though one of the groups has agreed a ceasefire with the government.
Mohamed Osman Hashim, the commissioner of Kulbous, a town next to Sudan's border with Chad, told Reuters some 2000 fighters from the Sudan Liberation Movement/Army (SLM/A) and the Justice and Equality group carried out the raid on Wednesday.
The SLM/A, which emerged as a fighting force in February, accuses the government of marginalising the western Darfur region. They were not immediately available for comment.
They entered peace talks after agreeing to a ceasefire in September, but have accused government forces and what it says are pro-government fighters of violating the truce.
SLM/A officials have said they were in talks to join ranks with the Justice and Equality group, which the government said it had targeted with air strikes earlier this month.
The United Nations is seeking more aide for western Sudan, where fighting has displaced at least 500,000 refugees this year. Sudan's government is also in talks to end a separate, 20-year-old conflict in the south.