Rwanda has issued an international arrest warrant for a top former Rwandan military official, Aloys Ntiwiragabo, who is under investigation in France over his role in the country's 1994 genocide which claimed 800,000 lives.

"We have issued an international arrest warrant against Aloys Ntiwiragabo, the genocide suspect. We have investigated his case and we are working with the French unit in charge of combating war crimes and crimes against humanity," prosecutor-general Aimable Havugiyaremye told a press conference on Tuesday.

France opened a probe into alleged crimes against humanity by Ntiwiragabo after he was found in the suburbs of the city of Orleans, about 100 kilometres south-west of Paris.

French investigative news site Mediapart tracked down the former Rwandan spy chief, who had been identified by the International Criminal Tribunal for Rwanda (ICTR) as one of the architects of the genocide.

Neither the ICTR, Interpol, France nor Rwanda were actively seeking him now and had dropped arrest warrants years ago.

The revelation of his whereabouts came barely two months after another suspected genocide architect, Felicien Kabuga, was arrested on the fringes of Paris.

Kabuga, who evaded police in several countries for 25 years, is accused of financing the genocide.

Kabuga had asked for a trial in France, citing frail health and claiming the UN court in Africa would be biased against him, and possibly hand him over to Rwandan authorities.

A team of prosecutors and investigators from the international tribunal handling Rwanda genocide matters arrived in Kigali Tuesday for a two-week visit to investigate and gather evidence on Kabuga and other genocide suspects at large.

France has long been known as a hiding place for wanted genocide suspects and French investigators currently have dozens of cases underway.

A plane carrying President Juvenal Habyarimana, from Rwanda's Hutu majority, was shot down in Kigali on April 6, 1994, unleashing the killing spree that would leave mainly Tutsis but also moderate Hutus dead.