Lieutenant-Colonel Felix Kulayigye, a spokesman for the Ugandan army, and a diplomat at the Rwandan embassy in Kampala confirmed the capture.
"Idelphonse Nizeyimana has been arrested," Kulayigye told the AFP news agency.
Nizeyimana, nick-named the Butcher of Butare, served as an intelligence officer in the Rwandan army in the southern town of Butare at the time of the genocide.
About 800,000 Tutsis and moderate Hutus were massacred by machete-wielding Hutus, also known as Interahamwe, in the genocide that lasted 100 days.
Nizeyimana is accused of having been one of the two leading organisers of the genocide in Butare, a university town.
He is on the wanted list of the ICTR and on a US list of Rwandan genocide suspects for whose capture a reward of $5,000 is offered.