In a deal reached last week, Khartoum lifted restrictions on Ugandan military operations against the LRA in southern Sudan as long as they are co-ordinated with its army and the south's former rebel movement, now part of a Sudanese unity government, it said.
Felix Kuraije, the deputy spokesman for Uganda's army, said the agreement allows Ugandan soldiers to move against the LRA in southern Sudan north of the so-called "red line," about 100km inside Sudanese territory, delineated in a 2002 cooperation pact between Khartoum and Kampala.
"The agreement means that the LRA will have nowhere to hide and that they will now face three forces," he said. "We are allowed to use our aircraft but they have to be co-ordinated with the ground forces and intelligence."
Kuraije said senior military officials from the cooperating armies would meet on Wednesday in the southern Sudanese town of Juba to plot strategy against the rebels who have often moved north of the red line.
In addition to allowing Uganda to move on the LRA throughout southern Sudan, the deal formally brings on board the ex-rebel Sudan People's Liberation Army (SPLA), which signed a landmark peace deal with Khartoum in January, he said.
SPLA participation in the fight is key to rooting out the LRA from bases in southern Sudan as it troops have detailed knowledge of the territory where the rebels often seek refuge north of the red line from Ugandan patrols, he added.
The pact was signed on Friday, just a day after United Nations officials said the International Criminal Court (ICC) had issued arrest warrants for five top LRA commanders, including its elusive supremo Joseph Kony, on war crimes charges.
Tens of thousands of people have been killed and more than 1.6 million displaced in northern Uganda since the LRA took leadership of a regional rebellion against Kampala in 1988.
Kony and his forces have been accused of massive abuses in the region including the abductions of at least 20,000 children who are used as porters, fighters and sex slaves for LRA commanders.
The Hague-based ICC, the first-ever permanent treaty-based international criminal court, has the mandate to prosecute individuals for crimes against humanity, genocide, war crimes and crime of aggression.
It assumed the jurisdiction to investigate serious war crimes in northern Uganda last year after Museveni referred the matter to the court.
Kony's alleged crimes include torture and mutilation, abduction, sexual violence, forced recruitment and the killing of people the LRA considers are supporters of Museveni.