The Ugandan army says it has resumed operations to hunt down Lord's Resistance Army (LRA) rebels in northern Uganda, despite peace talks.
Mr Kony's army fought the Ugandan government for almost two decades
Rebels only partially met a September deadline to leave the bush and gather in neutral zones in southern Sudan.
"They have abused the cessation of hostilities agreement," the army said.
An army spokesman said the move should not derail talks between the government and rebels, which are seen as the best chance of ending the 20-year conflict.
"This has nothing to do with the peace process which should continue," Maj Felix Kulayigye said.
He pointed out that according to the terms of a ceasefire deal, LRA fighters should have assembled in the holding camps in southern Sudan more that a fortnight ago.
"They have failed to do so," he told the BBC. "We can't just fold our arms and do nothing."
"If they are found outside the camps, they are a legitimate target."
He said army troops would now go back to the positions they withdrew from following the signing of a truce.
"For the last 34 days we have religiously observed the cessation of hostilities. However the time must come when we continue with our work."
The deputy spokesman for the rebel LRA's mediating team, Godfrey Anyap, told the BBC that the LRA forces would not fight back if attacked by the Ugandan army:
"As far as we are concerned we consider what they have just announced, which we have also seen in the newspapers, as an indication that the government of Uganda does not want to proceed with the peace negotiations," he told the BBC's Focus on Africa programme.
Earlier, LRA deputy rebel chief Vincent Otti said they needed more time to move fighters still left in northern Uganda.
Rebel fighters are supposed to be in two camps in southern Sudan to the east and eest of the River Nile.
Diplomats say that more than 1,500 fighters are now in the area of the camps - although the LRA are concerned that they could be attacked by Ugandan troops, and so live a few kilometres outside the designated camps.
The Ugandans are said to have close to 1,000 troops in southern Sudan, ensuring that the LRA does not infiltrate back into the country
The rebels have abducted thousands of children and forced them to fight since the conflict in the north began two decades ago.
More than one million people have fled their homes because of the fighting.
The peace talks taking place in Juba in southern Sudan have been characterised by deadlock and rumours of walk-outs, but mediators remain optimistic, with discussions under way on social development and political issues.