Since the National Resistance Movement (NRM) government came to power in January 1986, Uganda has witnessed several confrontations between the state and military officers who once served in the National Resistance Army (NRA) and later rose through the ranks of the Uganda People’s Defence Forces (UPDF).
Some of these officers were among the commanders who fought alongside President Yoweri Museveni during the five-year guerrilla war. Others joined the NRA after the change of government, while several later occupied influential positions as army commanders, intelligence chiefs and senior security officials.
However, their military careers have not always been characterised by loyalty and promotion. Over the years, some have been arrested, detained, court-martialled or prosecuted over allegations ranging from treason, rebellion and terrorism to insubordination, corruption, abuse of office and mismanagement of military resources.
The arrest of retired Lieutenant General Peter Elwelu in Soroti City on November 2, 2026, has once again brought this history into focus, adding another senior military figure to a growing list of former commanders who have faced serious confrontations with the government they once served.
The following are some of the notable officers and former military commanders who have faced such cases since 1986.
One of the earliest notable cases involved Lieutenant Colonel Ahmed Kashilingi, an NRA bush-war veteran who was arrested and charged with treason and misprision of treason in the early 1990s.
Kashilingi reportedly spent approximately five years in prison before being acquitted in February 1995.
His arrest also implicated another prominent bush-war commander, Colonel Julius Chihandae, who was accused of obstructing security personnel who had been deployed to arrest Kashilingi in January 1990.
Chihandae was subsequently charged with treason before the General Court Martial. Prosecutors alleged that he had helped Kashilingi evade arrest and escape security operations.
He was eventually acquitted and later returned to public service, including diplomatic assignments. New Vision+1
Another important case from the early years of the NRM government involved Brigadier General Moses Ali, a former leader of the Uganda National Rescue Front (UNRF) who joined the NRA after the collapse of the previous government.
Ali was serving as Minister of Youth, Culture and Sports when he was arrested on April 7, 1990, and charged with treason, terrorism and illegal possession of firearms.
He spent approximately 26 months in detention. Although he was acquitted of terrorism, he was initially convicted of illegal possession of firearms and sentenced to two-and-a-half years in prison in January 1991.
The conviction was subsequently overturned on appeal, and he was acquitted of the remaining treason charges in June 1992.
His case became one of the prominent examples of a former armed opposition commander who had joined Museveni’s government but later found himself facing serious criminal charges. Amnesty International+2
The early years of the NRM government also witnessed arrests involving military officers who had belonged to other armed groups before joining or operating alongside the new administration.
Among those affected were former officers associated with the Uganda Freedom Movement (UFM) and the Federal Democratic Movement (FEDEMU).
Some of the names documented in historical accounts include:
Captain Godfrey Nsereko, a former chief bodyguard to FEDEMU commander Captain George Nkwanga, who was arrested in Fort Portal and taken to Luzira Prison.
Captain Kamya Nkima, a former UFM officer who was arrested in Kampala.
Major Fred Kiberu Mpiso, a former FEDEMU commander based in Tororo, who was also arrested.
Major Aloysius Ndibowa, an officer associated with FEDEMU who reportedly went into hiding after some of his bodyguards were arrested.
Captain Paul Kavuma, Major Nsubuga and Lieutenant Nansera Lubega, former UFM commanders who were absorbed into the NRA’s 19th Battalion.
The arrests followed allegations of an attempted coup involving former UFM and FEDEMU officers.
The wider crackdown also involved civilian political figures, including former ministers and other government officials. However, the available historical accounts do not establish that every person arrested was convicted or that all the officers faced identical charges. Monitor+1
Another major confrontation involved former Army Commander Major General James Kazini.
In December 2003, Kazini and several senior military officers were taken before the General Court Martial over allegations involving fictitious soldiers on the army payroll and the diversion of military funds.
The investigations brought several other senior officers into the dock, including:
Brigadier Nakibus Lakara, former Army Chief of Staff.
Colonel Poteli Kavuma, former Second Division commander.
Lieutenant Colonel Dura Mawa Muhindo, former commander of the 507th Brigade.
Major Robert Nsabiyunva, former Director of Finance.
Colonel Stephen Othieno.
Lieutenant Kenneth Ayebale.
Captain Michael Baryaguma.
Captain Romeo Ndyabagye.
The allegations included inflating military payrolls with non-existent soldiers, diverting funds intended for recruitment and salaries, and misappropriating money allocated to military operations.
In October 2006, the General Court Martial withdrew abuse-of-office charges against Kazini, Lakara and five other officers.
Kazini, however, was subsequently convicted in March 2008 of causing financial loss to the UPDF and sentenced to three years in prison.
The prosecutions exposed questions about financial management, military recruitment and accountability within an institution responsible for handling substantial public resources. ugandaradionetwork.net+2
Former Security Minister Lieutenant General Henry Tumukunde is another prominent former military commander whose relationship with the government deteriorated.
Tumukunde previously served as Director General of the Internal Security Organisation (ISO) and held influential positions within the military establishment.
In May 2005, he was arrested and charged before the General Court Martial with conduct prejudicial to good order and military discipline after allegedly making unauthorised public statements during a radio appearance.
His subsequent disagreements with the military leadership included a dispute over his parliamentary position.
In 2013, he was convicted of military misconduct and received a severe reprimand.
His confrontation with the government resurfaced in March 2020 when he was arrested and charged with treason and other offences following public statements concerning a possible change in Uganda’s political leadership.
Tumukunde denied wrongdoing, and his case demonstrated how disagreements involving former senior security officials could develop into criminal proceedings. ULII+2
The fallout between the government and former military commanders became more pronounced around 2001 and 2002, when several NRA veterans went into exile and became associated with allegations of armed rebellion.
Among the most prominent were Colonel Samson Mande and Lieutenant Colonel Anthony Kyakabale.
Both had participated in the guerrilla struggle that brought the NRM government to power but later fell out with the military leadership.
They were accused of being involved in the formation of the Popular Resistance Army (PRA), an alleged rebel organisation that the government said was seeking to overthrow President Museveni.
Another officer associated with the fallout was Colonel Edison Muzoora, who was also reported to have fled with the other officers.
Mande and Kyakabale initially went to Rwanda before relocating to Sweden in 2003 amid diplomatic tensions between Uganda and Rwanda.
Their alleged involvement in the rebellion resulted in prosecutions against other suspected PRA collaborators.
In 2003, at least 25 people were reportedly charged with treason and concealment of treason in connection with the group’s activities.
Kyakabale eventually returned to Uganda in 2015, met President Museveni and was pardoned. He was later promoted to colonel before retiring from the army.
Mande, however, remained in exile.
The PRA episode remains one of the most significant cases involving former NRA commanders who turned against the political and military establishment they had helped create. Monitor+3
Former intelligence coordinator General David Sejusa, previously known as David Tinyefuza, also experienced a major fallout with the government.
Sejusa was among the influential military figures who served in the NRA and later occupied senior intelligence positions.
His disagreements with the military leadership became public in 2013, when he left Uganda and went into exile following controversy surrounding a letter attributed to him that raised concerns about alleged political succession arrangements.
He returned to Uganda in 2016 and was subsequently arrested.
He faced military charges including absence without official leave, insubordination, engaging in political activities contrary to military regulations and conduct prejudicial to military discipline.
Sejusa later officially retired from the army in August 2022 alongside other military officers.
His case added another former senior intelligence official to the list of military figures who experienced serious disagreements with the government. Monitor+1
Although General Kale Kayihura served primarily in the Uganda Police Force rather than as an army commander, his case is relevant to the wider history of former senior security officials facing prosecution under the NRM government.
Kayihura, who served as Inspector General of Police from 2005 to 2018, was arrested in June 2018 and faced proceedings before the General Court Martial.
The allegations included offences involving firearms and the alleged illegal repatriation of Rwandan nationals, including refugees and Ugandan citizens.
He was detained at Makindye Military Barracks before being granted bail.
In August 2023, the charges against him were withdrawn.
His case raised questions about the relationship between military courts, civilian security institutions and the prosecution of former senior security officials.
More recently, the prosecution of former Chieftaincy of Military Intelligence (CMI) chief Major General James Birungi brought renewed attention to accountability within the military intelligence establishment.
Birungi was arrested in August 2025 and subsequently charged before the General Court Martial alongside other senior intelligence officers.
Among those implicated were:
Peter Ahimbisibwe, formerly Director of Counter-Terrorism.
Ephraim Byaruhanga, formerly Director of Special Operations.
The officers faced serious allegations relating to treason, terrorism, corruption, murder and alleged manipulation of intelligence operations.
Prosecutors reportedly alleged that intelligence reports were fabricated, security alerts falsified and military resources improperly managed.
The allegations were contested, and the accused were entitled to defend themselves through the court process. edge.ug
Birungi’s case took an unexpected turn on October 22, 2026, when Chief of Defence Forces General Muhoozi Kainerugaba announced that he had forgiven the former intelligence chief and intended to secure his release.
The announcement raised questions about the legal status of the pending prosecution, particularly whether the charges would be formally withdrawn, dismissed or concluded through another lawful arrangement.
In September 2026, two other former intelligence chiefs, retired Major General Abel Kandiho and retired Brigadier General Charles Bakahumura, were also reportedly detained as investigations into alleged false intelligence and treachery widened.
Their detention further intensified scrutiny of the military intelligence establishment, although detention and investigation do not establish criminal guilt.
The prosecutions have not been limited to treason and political disagreements. Several other senior officers have faced charges involving the management of military resources.
In April 2026, Brigadier General James Barigye Ruheesi was charged alongside three other senior officers over the alleged misuse of approximately 270,000 litres of military operational fuel.
Colonel David Ocitti Kidega.
Major Innocent Kikongo Mugumya.
Captain Kenneth Labwon Kinyera.
The prosecution alleged that the officers had misused fuel intended for military operations for personal benefit, allegedly endangering operational efficiency.
The officers denied the charges.
The case highlighted continuing questions about the management of military logistics and public resources within the UPDF. Monitor+1
Another recent prosecution involved Major Nicholas Ntakirwa, also known as General James, who was charged alongside businessman Trevor Besigye and Mohammed Ali over an alleged $2.4 million gold transaction.
The accused faced charges of obtaining money by false pretences and scandalous conduct.
Although the case was not a treason prosecution, it illustrates the range of criminal allegations that have involved serving military personnel. New Vision
The latest development involves retired Lieutenant General Peter Elwelu, a former Deputy Chief of Defence Forces and former Commander of Land Forces.
Elwelu was arrested in Soroti City on November 2, 2026, following accusations by the military leadership that he was involved in subversive activities and alleged plans to destabilise the Teso sub-region.
His arrest followed public accusations by Chief of Defence Forces General Muhoozi Kainerugaba, who described him as a traitor and announced that he had stripped him of his military rank.
Acting Director of Defence Public Information Colonel Chris Magezi confirmed the arrest, saying security forces had apprehended the retired general following a manhunt.
According to Magezi, security forces had recovered 15 firearms, military fatigues and two pickup trucks allegedly linked to Elwelu.
He further said the former deputy army chief would be charged and prosecuted in accordance with the law.
The arrest followed reports that more than 20 former soldiers allegedly linked to Elwelu had also been arrested.
However, members of Elwelu’s family disputed allegations that he was organising an armed rebellion.
As of November 3, 2026, the UPDF had not publicly specified the exact charges Elwelu would face or provided comprehensive details of the alleged plot.
His arrest is particularly significant given his previous position in the military hierarchy and the fact that he once occupied some of the country’s most powerful security offices.
Looking at these cases, it is important to distinguish between officers who were convicted, those whose charges were withdrawn, those who were acquitted and those who remain under investigation or prosecution.
Moses Ali, Kashilingi and Chihandae faced serious allegations but were eventually acquitted of the principal charges against them.
James Kazini was convicted in a military financial misconduct case, while Henry Tumukunde received a military reprimand.
Kale Kayihura’s charges were withdrawn, while the cases involving Birungi and other intelligence officials have raised questions about how pending prosecutions should be concluded.
Mande and Kyakabale became associated with allegations of armed rebellion, although their subsequent experiences differed considerably.
The cases involving Elwelu, Kandiho and Bakahumura represent a more recent chapter in the relationship between former senior commanders and the military leadership.
Taken together, these developments demonstrate that the military establishment that emerged after 1986 has experienced significant internal disagreements, criminal investigations and confrontations involving some of its most influential former officers.
The repeated arrests and prosecutions of former senior commanders raise broader questions about the relationship between military discipline, political disagreements and accountability within Uganda’s security institutions.
The government has a responsibility to investigate officers suspected of treason, corruption, abuse of office or activities that threaten national security.
However, investigations and prosecutions must be conducted transparently, with respect for due process and the rights of accused persons.
There is also a public interest in understanding why some officers who participated in the liberation struggle and subsequently occupied senior military positions eventually found themselves facing criminal investigations or accusations of attempting to overthrow the government.
Equally important is the need to establish whether military prosecutions are consistently supported by credible evidence and whether the eventual outcomes are clearly communicated to the public.
Uganda’s military history since 1986 is therefore not simply a story of commanders who fought to bring the NRM government to power. It is also a story of internal conflicts, political disagreements, military prosecutions, corruption allegations and changing relationships within the country’s security establishment.
As Peter Elwelu becomes the latest former senior commander to face arrest, the bigger question remains whether Uganda’s military justice system can consistently demonstrate that no officer, regardless of rank, political connections or previous contribution to the country, is above the law — and that no individual can be punished without a fair and transparent legal process.
