An army spokesman said on Wednesday that the renewed operations in northern Uganda should not hinder negotiations between the two sides in neighbouring southern Sudan.
Major Felix Kulayigye said any Lord's Resistance Army (LRA) fighters in northern Uganda who had failed to assemble at two locations agreed under a truce that expired on September 19 would be "dealt with militarily".
"This has nothing to do with the peace process which should continue," he added.
The LRA - which began a civil war from northern Uganda 20 years ago - said it would defend its men against any army attack but that it remained committed to peace talks.
'We want to talk'
Vincent Otti, the movement's deputy leader, said by satellite telephone from the Sudan-Congo border: "If the LRA collide with the UPDF [Ugandan army], they will fight. That is what the UPDF wants. But for us, we don't want to fight, we want to talk.
Joseph Kony, leader of the LRA,
has been accused of war crimes
"The peace process will bring peace in northern Uganda."
Talks between Ugandan government negotiators and LRA representatives in southern Sudan had been widely viewed as the best chance to end the conflict that has killed tens of thousands and displaced nearly two million more.
A ceasefire signed in August committed the movement to gathering all their commanders and fighters at two assembly points in southern Sudan while the talks were held.
The LRA said that Ugandan soldiers were surrounding the Owiny-Ki-Bul assembly area near the Sudan-Uganda border, preventing them from reaching it, while the government accused rebels of drifting away from the camp.
Otti also said that some rebels were still hiding out in northern Uganda because poor communications in the remote area meant they had not received orders to gather at the camps.
Joseph Kony, the leader of the LRA, and Otti have refused to leave the bush unless the International Criminal Court (ICC) drops war crimes indictments against them.
The Hague-based court has repeatedly refused to drop the charges.
Talks stalled as both sides accused each other of breaking the ceasefire agreement, and the deadlock has prevented them from reviewing the truce and possibly extending it.
Negotiators for the LRA rejoined the talks on Friday, after walking out a day earlier.