In a national address delivered on Saturday, Museveni said concerns raised by the Inter-Religious Council of Uganda over alleged disappearances and illegal detentions had prompted him to explain what he described as the historical foundation of the National Resistance Movement's approach to justice and human rights.
The President revealed that religious leaders had expressed fears that Uganda risked sliding back to the human rights violations witnessed during the regimes of former presidents Idi Amin and Milton Obote.
He rejected that comparison, saying the current military operations under the command of Chief of Defence Forces Muhoozi Kainerugaba are fundamentally different because suspects are being arrested and presented before courts instead of being killed.
He argued that Ugandans should appreciate the work of the armed forces, saying security agencies are addressing long-standing gaps in law enforcement while respecting legal processes.
"The recent limited actions by security forces against some individuals and institutions are really long overdue actions to fill those gaps," Museveni said.
According to the President, the operations are intended to protect the peace achieved during the NRM's four decades in power while reinforcing economic progress by tackling corruption, criminality and impunity.
He accused what he described as "selfish people" and "agents of foreign interests" of undermining Uganda's development through misinformation and criminal activities, arguing that security agencies had been compelled to intervene after years of tolerance.
Museveni said he had often ignored personal attacks against him but claimed such campaigns had discouraged investment and tourism by creating what he described as a false image of Uganda abroad.
"Some people have been abusing Museveni, but Museveni has been ignoring them. That is true, but those malignments were slowing down our growth. Some investors and tourists are scared away from coming to Uganda on account of those false stories," he said.
The President further argued that weaknesses within the political, administrative and legal systems had allowed impunity to flourish, making stronger intervention by security agencies necessary.
He also defended Uganda's justice system by contrasting what he described as indigenous African concepts of accountability with inherited colonial legal traditions, which he criticised for allowing accused persons to evade responsibility through procedural protections.
Drawing extensively on his experiences during the National Resistance Army's guerrilla war, Museveni recounted historical cases in which soldiers accused of murdering civilians were publicly executed, saying those actions helped establish public confidence in the rebel movement's commitment to justice.
He said the current campaign is part of a broader government counter-offensive against corruption, organised crime and abuse of public office.
Museveni cited investigations that uncovered bribery networks operating around State House, saying the government had arrested individuals accused of demanding millions of shillings to facilitate access to presidential documents after information was provided by State Minister Fred Byamukama.
The President maintained that the security operations are designed to preserve peace, protect Uganda's development gains and ensure that no one uses legal loopholes to shield criminal conduct.