It quoted an official as saying the torching of the grass-thatched huts was intended to discourage "the voluntary return programme of the IDPs (displaced) to their villages by showing that there is no security and stability in the region".
The centre did not name the rebel group responsible for the attack.
Khartoum and the rebels regularly accuse each other of violating a ceasefire agreement they signed last year.
As many as 300,000 people are believed to have died in more than two years of civil strife pitting government forces and their Arab militia allies against ethnic minority rebels in the region.
The conflict has also displaced more than two million people, according to the United Nations.