The former Defence Intelligence and Security (DIS)—the military intelligence agency formerly known as the Chieftaincy of Military Intelligence (CMI)—once responsible for one of the country’s most sensitive security institutions, is now facing accusations that go to the heart of the credibility of the very intelligence system he previously commanded.
The development has attracted attention because Gen Birungi is also among the security officials expected to feature in the State’s case against former presidential candidate Dr Kizza Besigye and Hajji Obeid Lutale, who were arrested in Nairobi, Kenya, on November 16, 2024, and later charged with offences including treason.
The legal irony has been highlighted by human rights lawyer Eron Kiiza, who described the development as an unprecedented moment in Uganda’s military intelligence history.
“This historic detention—marking the first time a former CMI chief has been imprisoned—stems from a high-level board of inquiry that uncovered systematic failures, including fabricated intelligence, misappropriation of military resources, and operational manipulation within the UPDF's intelligence apparatus,” Kiiza said.
“The officers who abducted Besigye — and a witness lined up to testify against him — have themselves been detained over the fabrication of intelligence, and now face the Court Martial,” he added.
Gen Birungi was arrested on August 29, 2025, alongside two former senior intelligence officers: Col Peter Ahimbisibwe, then Director of Counter-Terrorism, and Lt Col Ephraim Byaruhanga, then Director of Special Operations.
The trio, according to Kiiza, were detained following a high-level investigation led by Lt Gen Sam Okiding that examined alleged misconduct within the Uganda People’s Defence Forces (UPDF) intelligence structures.
They are accused of offences arising from alleged failures in intelligence operations, including claims that intelligence reports were manipulated or fabricated. Among the allegations cited by Kiiza was a 2023 incident involving claims about the death of Allied Democratic Forces (ADF) bomb-maker Meddie Nkalubo, which investigators reportedly questioned.
The accusations remain matters before military courts, with the accused entitled to defend themselves against the charges.
However, the case has drawn wider attention because of its intersection with the ongoing treason proceedings involving Besigye and Lutale.
Besigye and Lutale have already filed a constitutional challenge against aspects of their prosecution, arguing that their arrest in Nairobi amounted to an unlawful abduction and extraordinary rendition.
In the court documents, they accuse security agencies of violating their constitutional rights by removing them from Kenya, detaining them at Makindye Military Barracks, and subjecting them to proceedings they argue were unlawful.
Their application names, among others, Lt Col Byaruhanga and Col Ahimbisibwe as respondents alongside Gen Muhoozi Kainerugaba and the Attorney General.
The applicants argue that their arrest and subsequent detention violated several constitutional protections, including rights to liberty, fair trial, protection from torture and the presumption of innocence.
The application states that “the purported trial and indictment of the Applicants on the counts of treason and misprision of treason is a violation of the principles of fair trial, human rights, the rule of law and extradition law, and is accordingly null and void.”
They further ask the High Court to declare that they were subjected to “extraterritorial abduction and extraordinary rendition from Nairobi, Kenya, to Uganda on 16th November 2024.”
The applicants also contend that their detention at Makindye Military Barracks was unlawful because it was a military facility not designated for holding civilians.
The court documents state: “The Respondents' four-day incommunicado military detention of the civilian Applicants in Makindye Military Barracks violated their right to personal liberty.”
They also allege that the detention denied them access to lawyers, family members and medical assistance, claims that the State is expected to contest.
The legal battle now presents an unusual situation: the credibility of intelligence evidence in the Besigye treason case is being examined at the same time that senior officers involved in Uganda’s intelligence system face accusations of compromising that system.
Gen Birungi’s position makes the situation particularly significant. As former CMI chief, he occupied a central role in the military intelligence chain of command during the period leading up to Besigye’s arrest.
His name appeared in discussions around the State’s case because he was expected to be among witnesses who could provide evidence about intelligence gathered by security agencies.
Yet, his own prosecution has introduced questions about the reliability, management and verification of intelligence produced during his tenure.
The charge sheet against him accuses him of offences connected to compromising military intelligence operations. It follows a wider investigation into alleged misconduct within military intelligence structures.
Kiiza described the situation as a major institutional contradiction.
“The officers who abducted Besigye — and a witness lined up to testify against him — have themselves been detained over the fabrication of intelligence,” he said.
The case against Gen Birungi also comes at a time when Uganda’s security institutions are undergoing internal scrutiny. His arrest was interpreted by observers as part of efforts by the military leadership under Gen Muhoozi Kainerugaba to address alleged misconduct within the armed forces.
The prosecution, however, will now have to deal with the wider implications of the allegations. Any challenge to the credibility of intelligence processes could become significant in cases where intelligence evidence forms part of the State’s argument.
For Besigye and his lawyers, the developments strengthen their argument that the circumstances surrounding his arrest and prosecution require judicial scrutiny.
For the State, the charges against Gen Birungi and his co-accused represent an attempt to enforce accountability within military structures and do not automatically invalidate intelligence gathered during their service.
The competing legal arguments will ultimately be tested before the courts.
But beyond the individual cases, the arrest of a former head of military intelligence who was also expected to appear as a witness in a major treason trial has created one of the most unusual intersections between Uganda’s national security system and its criminal justice process.
A security official once tasked with safeguarding intelligence now finds himself at the centre of a legal battle over whether that same intelligence system was compromised.