Rwanda has accused Mozambique, Malawi and Zambia of being unwilling to co-operate in hunting genocide suspects.
Bosco Mutangana, head of the unit tracking those suspected of involvement in the 1994 killings, told the BBC they all had files and arrest warrants.
But he said hundreds of "fugitives" were living in Southern Africa despite many diplomatic attempts to have them extradited to face prosecution.
Some 800,000 Tutsis and moderate Hutus were killed in the 100-day massacre.
Mr Mutangana said Rwanda's chief prosecutor had visited Mozambique and Zambia twice, in 2007 and 2009, and were still waiting for an appointment from the authorities in Malawi.
"They have the dossier of the names, where they're living, but we notice they don't want to do anything about it," he told the BBC's Great Lakes Service.
He said in comparison to how Europe has dealt with requests from Rwandan prosecutors, African countries were dragging their feet.
He said after handing over the files, Southern African officials had been invited to Rwanda but they had failed to come and carry out their own investigations into the allegations.
Those most responsible for the genocide are being tried by the International Criminal Tribunal for Rwanda (ICTR) based in Arusha, Tanzania.
Several other countries - including Canada, Finland and France - have tried genocide suspects rather than extradite them to Rwanda where they fear they may not get a fair hearing.