Uganda's army commander says his troops have been given unlimited access to fight Ugandan rebels based in Sudan.
The Ugandan army has been fighting the LRA for 19 years
The move follows last week's indictment of five Lord's Resistance Army rebels by the International Criminal Court.
Until now the army could not go beyond a so-called "red line", about 100km (62 miles) into Sudanese territory.
The Khartoum government backed the LRA until the end of Sudan's civil war, but the rebels remain active - their latest attack was reportedly on Friday.
The LRA, who abduct children to fight for them, has been waging a war in northern Uganda with no clear agenda for the past 19 years.
A priest said the rebels killed 10 women and six men who were farming outside Liria, 50km south-east of southern Sudan's capital, Juba.
"The LRA attacked them when they were cultivating," Reverend Paul Yugusuk of the Sudanese Anglican Church said.
The BBC's Will Ross in Kampala says that Ugandan Defence Minister Amama Mbabazi named this area, which is 60km beyond the "red line", as the location of LRA leader Joseph Kony on Friday.
Uganda's army commander, Lt Gen Aronda Nyakairima, said the new protocol allows Ugandan soldiers to operate wherever the LRA is situated in Sudan.
"Joseph Kony is now the 'red line'. Wherever he is we shall go there," he told the BBC.
He said the protocol was signed by the Ugandan and Khartoum military and also for the first time by former Sudanese rebel group, the SPLA.
While the LRA was backed by Sudan's government, Uganda used to offer support to the SPLA.
But with the end of Sudan's civil war in January this support has officially ended and the Sudanese military has been allowing the Ugandan army limited access into Sudan.
Lt Gen Nyakairima also said he was disappointed that the Congolese military had not attacked the LRA rebels on their territory before they fled the Democratic Republic of Congo back to Sudan.