"4,000 refugees crossed into Uganda through Bunagana border," the Red Cross said in a statement Friday.
No new arrivals were recorded on Friday however, spokeswoman Catherine Ntabadde-Makumbi told AFP by telephone from Uganda.
The Ugandan authorities encouraged the refugees to move to a nearby transit camp.
"Some have accepted to move but most prefer to stay at the border for now," in order to see how the security situation on the Congolese side of the border evolves, Ntabadde-Makumbi told AFP.
A source in Kisoro, a Ugandan town not far from the border said those who crossed were from Kyanja, a village 25 kilometres (17 miles) from the border and that they were fleeing fighting between two factions of the M23 rebel group.
The source in Kisoro said many of those who fled hoped to be able to return home in the next few days.
"A large number of these newly arrived people... prefer to stay near the border to monitor the situation in order to return. Many feel that the situation will calm down within the next day or two and hope to go back," the source said.