Amnesty International has reported allegations of arrests of members of the Fur and Zaghawa ethnic groups during fighting between the army and rebels in the areas of Kuttum and Teinah.
In a statement on Tuesday night the organisation said: "In the whole of the Darfur region... the Sudanese authorities have resorted to arresting and detaining incommunicado many people suspected of sympathizing with the armed group."
However, the accusations could not be independently verified or confirmed with Khartoum.
Darfur is an isolated and partially desert region on Sudan's border with Chad where perceived government support for Arab militias has spawned a rebellion among non-Arab communities.
"The Sudanese authorities have resorted to arresting and detaining incommunicado many people suspected of sympathizing with the armed group"
The rebel Sudan Liberation Movement (SLM) announced on Tuesday it had withdrawn its forces from Kuttum which it captured on August 1.
The movement, which is fighting for an independent state, said it took the decision to spare the town's inhabitants the casualties which would have followed a government assault.
The SLM began life as the Darfur Liberation Movement in August 2001 before re-emerging under its current name in February when it began claiming responsibility for a series of anti-government attacks.
Sudan has been racked by civil war for the past 20 years.
Accusations of atrocities and human rights abuses are frequently levelled by both Khartoum's Islamist regime and the rebels.