One of the most wanted suspects in the Rwandan genocide, which left some 800,000 people dead, has been arrested in the Ugandan capital, Kampala.

Former intelligence chief Idelphonse Nizeyimana stands accused of organizing the killing of thousands of ethnic Tutsis — including the revered former queen during 100 days of slaughter in 1994.

Nizeyimana was arrested while travelling to Kenya through the Democratic Republic of Congo and was immediately flown to Arusha, Tanzania, to face trials in the International Criminal Tribunal for Rwanda (ICTR), Ugandan police said Tuesday.

Officials in Tanzania are yet to confirm the arrest, but described Nizeyimana as one of their most wanted targets.

According to the tribunal, he is charged with setting up roadblocks where people carrying Tutsi ID cards were hacked to death with machetes, and helping draw up death lists of Tutsis.

He also allegedly ordered soldiers to kidnap a group of refugees, including 25 children and two priests from a convent, who were never to be seen again.

One of his units is believed to have killed Queen Rosalie Gicanda, widow of King Mutara III who died in mysterious circumstances in 1959 shortly before the Rwandan monarchy came to an end.

According to human rights reports, Hutu soldiers took the 80-year-old queen along with several other women from her house and shot her dead behind the national museum in the south-eastern town of Butare.

Two days later, the queen's mother was also murdered.

Most of the former Rwandan military and Interahamwe militia members responsible for the genocide fled to Rwanda's giant western neighbor, DR Congo, after Tutsi rebels came to power in July 1994 and ended the carnage.

Their presence in eastern Congo sparked a war and a humanitarian catastrophe that has killed at least 5.4 million people over the past decade.