LRA 'to retaliate'
David Nyekorach-Matsanga, the spokesman for the rebels, told Al Jazeera: "This is a highly regrettable provocation and the LRA will retaliate. This was perpetrated by militarists within the Ugandan army who want to destroy the peace process.
"We can't negotiate when people are trying to attack us. This is every bad precedent.
"Ankunda is one of those militarists who never wanted peace to return to Uganda."
The UN peacekeeping mission in the Congo, Monuc, said it had been warned of the operation but was not involved.
Kampala last week accused the DRC of failing to track down Kony and his lieutenants.
The rebel leader has reneged on a peace deal already agreed by the Ugandan government and has been hiding in the eastern DR Congo.
Tens of thousands of people have been killed and nearly two million displaced in the two decades of fighting between the LRA and the Ugandan government.
Uganda's civil war effectively ended in 2006 when a peace process was launched but Kony and his top commanders have remained elusive and continued to commit atrocities in remote areas of neighbouring countries.
Kony, a semi-literate former altar boy, took charge in 1988 of a regional rebellion among northern Uganda's ethnic Acholi minority.
He is accused - along with his top commanders - by the International Criminal Court (ICC) of raping, mutilating and murdering civilians as well as forcibly recruiting child soldiers.