The innovative answer was to revive the concept of the customary "courtyard" or "gacaca" hearings and 11,000 of these courts were set up.
All but the top tier suspects - the planners and instigators of the genocide, notorious mass murderers and rapists who were sent to a United Nations tribunal - went to gacaca courts where witnesses could confront accused perpetrators.
The Government of President Paul Kagame said the courts were intended to re-establish a "concord" and enable "the simple citizens who have been manipulated and have perpetrated the crimes to take a good start again".
Authorities vowed that justice could "become true only if the truth about the events is established".
However, while this week's report acknowledged the extraordinary scale of the problems faced by Rwanda and some local acceptance of the gacaca solution, it said that the justice they gave was allowed "only insofar as it did not threaten the existing political order".
Kagame's Rwandese Patriotic Front, in power since 1994, has always claimed credit for stopping the Hutu-led genocide.
But the President's reputation has lost some of its shine since the Government was accused of a violent crackdown before last year's elections, sending hit squads to assassinate regime critics in Britain and South Africa among other countries.
Kigali has denied murdering Rwandese critics living abroad and accused European and United States critics of imposing Western democratic models on a fragile state.
In its own report on the gacaca system this year, Human Rights Watch said the courts had done well to process so many cases and alleviate prison overcrowding but had done so at the expense of fair trials and had failed to address crimes by Tutsi rebels.
The unusual source of this week's criticism of one of the central planks of Kagame's success story - coming from traditionally quiet donor Japan - will embarrass Kigali.
Jica handed out US$33 million ($39.3 million) in grants to Rwanda last year.
- INDEPENDENT