The United Nations Refugee Agency (UNHCR) says 8,000 people have crossed into Uganda to escape the latest fighting in eastern Congo.
Thousands have left their homes in the past week
The villagers were caught in crossfire as the Congolese army moved against the forces of renegade General Laurent Nkunda and other militias.
Like Nkunda, the leader of the Mai Mai militia also rejected a government ultimatum to disarm.
More than 370,000 people have been displaced since the start of the year.
It is the third time in recent months that large numbers of people have fled to Uganda because of renewed fighting.
The UNHCR says the refugees are trying to remain close to the frontier so they can return home as soon as possible.
Moving against militias
The Mai Mai leader, Kasereka Kabamba, told the BBC his militia was helping the government fight Gen Nkunda, and his men would not be disarmed before General Nkunda's men did the same.
KEY FORCES IN THE KIVUS
FLNK - new group made up mainly of Congolese Mai Mai with some Rwandan Hutus formerly in the FDLR
FDLR - Hutu militia made up of former Rwandan soldiers and others who fled into Congo after the 1994 genocide
FARDC - Congolese army
Gen Laurent Nkunda, with an estimated 5,000 soldiers
Monuc - UN Mission in the DR Congo
The Congolese army commander in the Kivus says the Mai Mai militia is hindering the government's campaign.
Col Delphin Kahimbi said he had given Kabamba Kasereka "48 hours to lay down his weapons and turn over the men under his command to reintegration centres".
Gen Nkunda says he is defending Congolese Tutsis and has cited the presence in the region of other militia groups as a reason for not disarming.
He has accused government forces, Mai Mai militia and Rwandan Hutu rebels operating in the area of colluding against him.
The government denies this, and says it has run out of patience with Gen Nkunda who ignored a Monday deadline to begin disarming his troops.