The genocide saw militias from the majority Hutu ethnic group killing Tutsis and moderate Hutus.
Prosecutor for the International Criminal Tribunal for Rwanda (ICTR) Hassan Bubacar Jallow told the BBC's Focus on Africa radio programme that Mr Ntaganzwa was "a big fish", even if he was not the most senior person to have been caught.
The ICTR indictment describes his involvement in 1994 in the killing of more than 20,000 Tutsis between 14 and 18 April.
It says he "substantially participated in the planning, preparation and execution of the massacre".
He told a group including Hutu civilians to surround Cyahinda parish, in southern Rwanda, "so that no Tutsis could escape and told them to kill Tutsis", the indictment adds.
He is also wanted for other crimes.
The ICTR, which is now winding up its activities, has transferred his case to Rwanda, Mr Jallow told the BBC.