Some 4,000 are staying with relatives in Kisoro, in western Uganda. Another 1,680 Congolese refugees have moved to Nakivale settlement camp in central Uganda.
While representatives of the new arrivals said they are not yet in need of assistance, UNHCR is creating contingency plans for an influx of up to 100,000 people.
Uganda Disaster Preparedness Minister Musa Ecweru told IRIN that refugee traffic was very fluid.
"What we've witnessed over the years is that they can be 10,000 today, but then 4,000 will leave if they think the situation is stabilized. The number fluctuates," he said.
"These are human beings, and they are not coming for a holiday, they are coming because they are persecuted. We must received them and treat them as human beings whether or not we have resources and capacity," he added.
The primary areas of concern for UNHCR are food resources and medical capacity. UNHCR is partnering with the Government of Uganda, WFP, UNICEF, MSF and other organisations to plan for future influxes.
"We remain in daily contact with border and district authorities in Kisoro and we would be ready to intervene within 24 hours by setting a Transit Centre to deliver emergency assistance to the Congolese refugees, if the situation deteriorates and the refuges will require our help," said Stefano Severe, UNHCR Representative in Uganda.
UNHCR is also planning an informational campaign that would inform refugees of their rights and options in the immediate future.
In October 2007, about 20,000 DRC refugees fled to Uganda, though only about 8,000 stayed and settled at the Nakivale camp in central Uganda.
Uganda has a strong legal framework for protecting refugee rights, but critics often argue that the country lacks the ability to execute these laws. In October 2008, there are about 147,000 refugees living in Uganda, 49,000 of them from DRC.