He is expected to stand trial before the General Court Martial, with charges reported to include treason, corruption, terrorism, and murder, according to local media.
Birungi's arrest follows an investigation led by Deputy Chief of Defence Forces Lt Gen Sam Okiding.
The inquiry was launched earlier this year to scrutinize alleged misconduct within the Uganda People's Defence Forces (UPDF), particularly in intelligence and counterterrorism operations.
Findings from the probe suggest that certain UPDF officers may have fabricated or exaggerated bomb threats in Kampala as a means to obtain funds or mask illegal dealings.
Investigators also looked into misleading intelligence reports, including a claim about the death of ADF commander Meddie Nkalubo, information that had been verified under Birungi's leadership at CMI.
The senior officer was apprehended on Friday night and immediately transferred to Makindye Prison. His case marks the first time a former CMI chief has been jailed.
Birungi's military career has been turbulent in recent months. After being removed from CMI earlier this year, he briefly served as commander of the UPDF Mountain Division before being reassigned as a military attaché to Burundi, a role he never formally assumed.
IGIHE
