Ndahimana was a local administrator in the Rwandan town of Kivumu during Rwanda's genocide, in which around 800,000 Rwandan Tutsis and moderate Hutus were killed over 100 days in 1994.
According to Ndahimana's indictment by the International Criminal Tribunal for Rwanda, he is responsible for the deaths of at least 2,000 Tutsis, most of whom were killed when Hutus bulldozed the church where they were being held.
Prosecutors with the tribunal believe almost all of Kivumu's 6,000 Tutsi residents had been killed by July 1994.
The tribunal, based in the Tanzanian city of Arusha, was seeking Ndahimana's arrest for genocide or complicity in genocide, conspiracy to commit genocide, and crimes against humanity.
Twelve other ICTR indictees remain at large.
Mende said that Ndahimana was "now in the hands of the military's operational authorities awaiting his transfer to Arusha".
Most of the former Rwandan military and Interahamwe militia members responsible for the genocide fled the country after Tutsi fighters swept through the country, ending the killing.
Their presence in eastern Congo, Rwanda's giant western neighbour, served as a pretext for two Rwandan interventions, which sparked a 1998-2003 war and humanitarian catastrophe that has claimed 5.4 million lives over the past decade.
Relations between the former enemies have improved dramatically since late last year.
In December, Kinshasa allowed Rwandan soldiers to enter eastern Congo to take on the FDLR, whose ranks include some of the orchestrators of the genocide.
The Congolese army, with the backing of what is the world's largest UN peacekeeping mission, launched operations against the FDLR earlier in the year.
Human Rights Watch has condemned the operations' heavy toll on civilians, but on Wednesday it applauded the arrest of Ndahimana.