Ugandan officials shut down the Bunagana border post this week after complaints from the Congolese government that the M23 rebel group, which seized it in July, was using it to raise funds.
“The Congolese were complaining that M23 were taxing lorries and goods going through, so at the request of the government of Congo we have closed the border,” said Felix Kulayigye, a Ugandan army spokesman.
A leaked report from a United Nations group of experts has accused senior Ugandan officials of “actively” supporting the M23 rebels.
Kampala has reacted angrily to the allegation, threatening to pull out troops from international peacekeeping missions, including the African Union mission in Somalia, unless they are withdrawn.
The M23 was formed in May by former fighters in an ethnic Tutsi rebel group that mutinied after having been integrated into the DR Congo military under a 2009 peace deal.
They complained the terms of the deal had never been fully implemented.