Uganda has begun consultations on how to deal with rebels and others responsible for atrocities during the insurgency in the north of the country.
Mr Rugunda is looking at a system based on traditional values
Internal Affairs Minister Ruhakana Rugunda said they are seeking views from victims and legal experts on setting up war crime courts.
The government and Lord's Resistance Army rebels are engaged in peace talks in Sudan aimed at ending the conflict.
Some 1.7m people are living in camps in the north as a result of the fighting.
LRA leader Joseph Kony and his deputy Vincent Otti are among the five rebel commanders who have been indicted by the International Criminal Court for war crimes.
"The victims are the primary people concerning in this peace process, they are the ones who suffered and their views are critical in ensuring there is accountability and reconciliation," Mr Rugunda told the BBC's Network Africa programme.
Government officials have begun seeking views from people living in 10 towns in the north of the country where most atrocities were committed.
Mr Rugunda, who is also the government's chief negotiator at the peace talks, also hinted that there is a possibility of forming a unique legal system based on traditional values to set up local war crimes courts.
They will ask victims of the violence throughout the northern towns how they believe the perpetrators should be punished, not only for the killings but for the brutal mutilations and abductions carried out by Lord's Resistance Army rebels, who cut the lips and tongues from civilians and took their children off to fight or serve as sex slaves.
Journalist Oryema Lacambel of Mega FM told the BBC's Focus on Africa programme that over 250 people came to the first meeting in the town of Gulu.
He said people feel strongly about wanting an alternative justice system, though there was a sense that they were all wondering how it might work.
Some people thought the rebels should be forgiven, he explained, while others thought they should have some kind of punishment at least, "so that impunity is not promoted in our land".
Mr Lacambel added that there were calls for the LRA and the government to meet and consult people together, and for the LRA to make contact with victims themselves.
LRA rebels have said they may accept the idea of setting up local courts but warned the government not to take unilateral decisions.
The rebels have vowed not to sign a final peace deal unless the ICC in The Hague withdraws arrest warrants for its leaders.
The peace talks in Juba were suspended last month to allow both sides to consult with the victims on the process of reconciliation and punishing those responsible for the atrocities.