A rebel group, the Lord's Resistance Army, rejected a truce meant to lead to peace talks, and has taken violent actions against the Ugandan army, the government said.
"Operations will not cease ever again until the Kony group irreversibly commit themselves to come out of the bush," Museveni told a gathered crowd in Gulu.
"It is the rebels who refused to sign the cease-fire memorandum of understanding and this is the reason why the government has taken the decision to start fighting them while the peace option remains," he said. However, the president also said negotiations will continue.
Third-party mediators said the LRA wanted more time to study the government's proposed memorandum of understanding, the BBC said.
The Lord's Resistance Army, led by Joseph Kony, has been accused of abducting more than 20,000 children. The government said the rebel group made the boys fight and the girls work as sex slaves. The group has also been charged with mutilating and burning civilians.
Some 1.5 million Ugandans have been displaced during 18 years of fighting.