Twenty-six years ago this month, President Yoweri Museveni dismissed four directors from the Internal Security Organisation (ISO), citing internal security lapses and dissatisfaction with performance amid escalating threats of terrorism. At the time, Lt Henry Baguma, Capt Herbert Kwiringira, Dr Asiimwe Rwekikiga, and Mr Stephen Ssenoga Ndahura—all long-serving Uganda People’s Defence Forces (UPDF) officers—were shown the door.
Each of the directors held a key portfolio within ISO: Lt Baguma oversaw finance and administration, Capt Kwiringira was in charge of defence, Dr Rwekikiga led economic affairs, while Mr Ndahura managed technical services. Their dismissal was announced on June 8, 1999, by then-ISO Director General Brig Ivan Koreta during an internal meeting. Letters confirming their removal were signed by then-Minister for Security, Mr Wilson Muruli Mukasa.
Following the shake-up, the directors were redeployed to various ministries. Lt Baguma became a personal assistant to Parliamentary Affairs Minister Rebecca Kadaga, Capt Kwiringira was appointed aide to Education Minister Khiddu Makubuya, Dr Rwekikiga joined the Agriculture Ministry under Dr Kisamba Mugerwa, and Mr Ndahura assisted Janat Mukwaya at the Ministry of Gender.
Several of these ministers have since left public service. Dr Makubuya, who later served as Attorney General, passed away in August 2024. Dr Kisamba Mugerwa succumbed to Covid-related complications in January 2021. Janat Mukwaya retired from elective politics in 2011, though she briefly returned as Minister for Gender in 2016 before exiting in 2019.
The dismissals came after President Museveni publicly criticized internal security operations, blaming lapses for a series of terrorist attacks. He raised these concerns during a cadet pass-out at the School of Infantry in Jinja earlier that year and reiterated them during the June 9, 1999 Heroes’ Day address at Kololo.
The tipping point was a pair of bomb blasts on February 13, 1999, in Kabalagala, Kampala, where four people, including an Ethiopian student, were killed. Homemade pipe bombs exploded in two bars during Valentine’s Day celebrations. Among the injured were foreigners, including a USAID consultant and several European nationals. Though no group claimed responsibility, a government official reportedly linked the attacks to the Allied Democratic Forces (ADF), a rebel coalition made up of Tabliq Islamist sect members, ex-soldiers from Zaire and Rwanda, and NALU fighters.
This wasn’t the first time Uganda had been rocked by such violence. In 1998, explosions in restaurants, bars, and public buses killed dozens. In one instance, 24 people died when bombs exploded on three buses leaving Kampala.
Behind the scenes, security agencies were locked in a turf war. A June 1999 report from The Monitor detailed conflicts between ISO, the police’s Special Branch (SB), and the Chieftaincy of Military Intelligence (CMI) over who should lead counter-terrorism efforts. CMI boss Col Henry Tumukunde reportedly criticized ISO and SB as ill-equipped to handle urban terror threats. The rivalry reached its peak as control of the counter-terrorism budget shifted from SB to CMI.
Before the realignment, SB had been receiving the full counter-terrorism budget and distributed portions to ISO and CMI, a system that bred resentment. The Treasury was instructed to channel all future funds directly to CMI, deepening the institutional divide.
A further point of contention emerged over the controversial use of “safe houses” for detaining suspects. ISO and SB opposed their reopening, wary of public backlash. Police eventually refused to take custody of detainees from such facilities. Notably, in late 1998, then-Internal Affairs Minister Maj Tom Butime told Parliament all safe houses had been shut, and Brig Koreta issued a formal apology, promising they would never be used again.
General Ivan Koreta, who managed ISO during this turbulent time, retired from the UPDF in August 2021, concluding a military career that spanned decades. His exit came alongside the retirement of 13 other generals and hundreds of officers from various ranks.
President Museveni’s latest dismissal of ISO officials in 2025 amid new counter-terrorism concerns evokes memories of 1999’s internal security reset. It reflects a continuing pattern where lapses in security prompt sweeping purges, institutional rivalries, and resource reallocations—all under the shadow of Uganda’s ongoing fight against terror threats.