"There has been a lot of shooting, this is why we have fled," a refugee told the BBC.
Fighters loyal to Ntaganda reportedly clashed with DRC forces in the east of the country.
BBC correspondents said they witnessed a steady stream of families fleeing the fighting.
The International Criminal Court in 2010, in an unsealed indictment, accused Ntaganda, a former military commander, of crimes committed in the DRC. The ICC said there was "reasonable grounds to believe" he played a direct role in conscripting child soldiers.
DRC was marred by violence following presidential elections in November. Media reports last month suggested Ntaganda was planning to launch a full-scale rebellion against DRC forces.
The Congolese military, the BBC reports, said its forces were overwhelmed by Ntaganda loyalist in the east of the country.