The Ugandan army says the Lord's Resistance Army (LRA) led by Joseph Kony is being supported and supplied by the Sudanese government.
The LRA is accused of rape, mutilation, murder and the recruitment of child soldiers.
A Ugandan army colonel told the BBC they had captured a member of the LRA who was wearing a Sudanese uniform, and carried its weapons and ammunition.
Sudan's ambassador to London has denied the allegations as "a big lie".
"We are not helping and we will not help [Joseph Kony]. He's a criminal," ambassador Abdullahi al-Azreg told the BBC's Newshour programme.
The US has sent special forces to help in the hunt for Mr Kony.
The 100-strong mission is working in four bases across Central Africa, where the LRA is moving in small groups, raiding and abducting villagers to become fighters, sex slaves or porters.
An online video produced by the US pressure group Invisible Children earlier this year helped raise international awareness of the LRA's activities.
Last month the African Union set up a 5,000-strong force to track down the fugitive warlord.
Mr Kony and his close aides have been wanted for war crimes by the International Criminal Court since 2005.
Ugandan army spokesman Col Felix Kulayigye told the BBC it had information that the LRA was now moving into Sudan, including areas of Darfur controlled by the pro-government Janjaweed militia.
"Kony knows we can't enter that region, so when the pressure is high in Central Africa he crosses into the Sudanese border [areas]," he said.
During Sudan's two-decade civil war, Uganda supported rebels who last year led South Sudan to independence. Meanwhile, Sudan's government was widely believed to have supported the LRA in order to weaken the Ugandan military capability.
A senior Ugandan military commander recently said his country might intervene if war broke out between the two Sudans, implying it would be on the side of the South.
Mr Kony, whose army first emerged in northern Uganda, has evaded capture for more than 20 years as his forces terrorised large areas of Central Africa.
He claims he has been fighting to install a government in Uganda based on the Biblical 10 Commandments.
Mr Kony was due to sign a peace deal with the Ugandan government in 2008, but peace talks fell apart because the LRA leader wanted assurances that he and his allies would not be prosecuted.
The BBC's Dan Damon is one of a few journalists who has visited the US forces based in Obo, Central African Republic.
He says fear of the LRA is tangible and real to people in Central Africa, especially in remote areas along the heavily forested and often unmarked borders between Uganda, the Democratic Republic of Congo, South Sudan and Central African Republic.
The US forces told the BBC that they were not hunting for Kony themselves, but assisting local armies and co-ordinating intelligence and communications.
Maria Wangechi, from the medical charity Merlin, says the LRA staged its most recent attack two weeks ago, but the presence of the US and AU forces has helped reassure civilians in the region.
The LRA has now split into small groups.
The BBC's Dan Damon says they do not use any form of electronic communications, but instead use runners and rendezvous points to keep in touch.
He says that means the US electronic surveillance technology may not be so useful as the hunt for Joseph Kony continues.