The move came a day after officials from both the government and the Lord's Resistance Army (LRA) said they were "very near" a deal to end their brutal, two-decade war and the two sides said the resumption of patrols would not affect ongoing peace talks.
Army spokesman Major Felix Kulayigye said Ugandan People's Defence Forces (UPDF) troops had returned to safe passage corridors after the expiration of truce provisions allowing the rebels to move to neutral camps in southern Sudan.
"The UPDF has resumed its duty to defend the Ugandan people," he told news agency AFP. "We have gone back to the positions we had withdrawn from under the cessation of hostilities agreement."
No resumption of hostilities
Major Kulayigye said the resumption of patrols was not a resumption of combat operations and had not yet resulted in any fighting.
But he said government troops would not stand by if the LRA resumed ambushes on civilian targets.
The army also said it was unclear if there were any LRA fighters still hiding in the bush in northern Uganda.
"We have sent squads to areas we withdrew from to make sure there are no (LRA) elements there that can cause trouble," said Lieutenant Chris Magezi, the army spokesman for the region.
Major Kulayigye and Lt Magezi and said the military had no plans to move beyond areas they had patrolled before the truce took effect.
Under the terms of the truce, the rebels were given three weeks to get to camps in southern Sudan via the safe passage routes and to remain there for the duration of the peace talks in the southern Sudanese capital of Juba.
The truce technically expired on September 19, when a scheduled review of the deal by a joint commission did not take place, although the government in Kampala said at the time it would be extended.
In Juba, a senior member of the LRA delegation to the talks said the patrols were a "side issue" that would have no effect on the negotiations but stressed that rebel forces would defend themselves if attacked.
"We have given instructions to our forces that they can only fight if attacked," Ayena Odongo told AFP, speaking for the LRA delegation. "We assure the people of Uganda and northern Uganda, in particular, that we shall not allow the region to be a battleground again."
"The major issue is the comprehensive agreement. Even if government declares a resumption of war, we shall continue with the peace talks," he said.
The Juba talks are seen as the best chance to end northern Uganda's 19-year conflict that has killed tens of thousands of people, displaced nearly two million and is referred to as one of the world's worst and most forgotten humanitarian crises.
Just days ago aid agencies and others warned the negotiations were at a crisis point, amid accusations of violations of the truce by both sides.
The sides are also split over war crimes charges filed by the International Criminal Court against elusive LRA leader Joseph Kony and four of his top lieutenants, one of whom is now dead.