The LRA are notorious for abducting children and mutilating victims
Ugandan Lord's Resistance Army rebels have carried out a surprise attack on a military base in southern Sudan.
There are also separate reports of LRA raids on three villages just over the nearby border with the Democratic Republic of Congo.
Roman Catholic priests in the region say the rebels abducted more than 50 children and burned down houses.
The fighting broke out despite pledges by the rebels that they would sign a peace deal with the Ugandan government.
The BBC's Africa analyst David Bamford says instability in the region appears to be growing as moves to persuade LRA leaders to sign the agreement falter.
The LRA has led a rebellion against the government for more than 20 years which has left some two million people displaced.
The group has relocated to camps on the Sudan-DR Congo border for the last two years during peace negotiations.
Earlier this month, the Congolese army sent troops to the region to try to protect civilians from the rebels.
A senior official in southern Sudan's Western Equatoria State government, Colonel Joseph Ngere, said the barracks attack involved about 100 LRA rebels.
He said it came as a complete surprise, adding that the rebels had also attacked the nearby village of Sakure.
The attacks in DR Congo are reported in the villages of Duru, Nambia and Kiliwa.
Several civilians are reported to have been killed.
Congolese troops have been reinforced in a nearby town.
In April, LRA leader Joseph Kony refused to sign a peace deal agreed to by his representatives after nearly two years of talks.
Mr Kony was said to have not signed the April agreement because he was seeking guarantees about arrest warrants from the International Criminal Court (ICC) in The Hague.
Last weekend, an LRA spokesman told the BBC the rebels were willing to sign the agreement but would not disarm until the ICC indictments were lifted.
The LRA leader is accused of numerous war crimes, including abducting and mutilating civilians and forcing thousands of children into combat.
Recent reports say he has set up six new bases in northern DR Congo and is running diamond mines in the Central African Republic.