"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.
Wisconsin business offering 'therapeutic cuddling' forced to close
Megyn Kelly: Santa Claus and Jesus are both white men