Rwanda has recalled its ambassador to France as the row between the two countries over culpability for the 1994 Rwandan genocide spiralled to a new low.

The decision to bring Emmanuel Ndagijimana home from Paris was made after a French judge issued arrest warrants for nine high-ranking Rwandans accused of involvement in the assassination of then-President Juvenal Habyarimana – an occurrence which triggered the mass slaughter.

The officials targeted by the arrest warrants are close to Rwanda’s current president, Paul Kagame, who was himself asked by the French anti-terror judge to stand trial over the murder of President Habyarimana, whose aircraft was shot down on April 6 1994.

In the wake of the plane crash, militants from the ethnic Hutu majority, known as the interahamwe, quickly set up roadblocks across the capital, Kigali, and on April 7 began the mass killing of Tutsis and moderate Hutus, murdering more than 800,000 people in 100 days.

The accusations by Jean-Louis Bruguiere – the examining magistrate in question – have infuriated the government of Mr Kagame, who is revered by many genocide survivors for eventually defeating the Hutu extremists and seizing back control of the country with his party, the Rwanda Patriotic Front.

Rwanda has accused Paris of making the allegations as a means of covering up its own role in training soldiers who carried out the genocide. Yesterday, 25,000 Rwandans protested in Kigali against France, accusing it of complicity in the slaughter – a charge Paris has always denied.

Tharcisse Karugarama, the Rwandan Justice Minister, said that the recall of its envoy was a response to French "bullying", accusing Paris of seeking to topple the government. He threatened further that Rwanda could sever ties with Paris completely.

"There is no reason why there should be diplomatic relations with a country that is actually attempting to destabilise the institutions of Rwanda’s government," he said.

Mr Bruguiere is investigating the case because the crew on Mr Habyarimana's crashed plane was French. The families of the pilot, co-pilot and mechanic, who all died in the crash, filed a suit in France in 1998.

The question of who shot down the plane has been a central mystery of the genocide. Speculation has focused on President Kagame’s largely Tutsi force, or hard-line Hutus hoping to encourage mass violence against Tutsis.

According to Mr Bruguiere’s order, Mr Kagame allegedly instructed his group to down the aircraft. "The final order to attack the presidential plane was given by Paul Kagame himself during a meeting held in Mulindi on March 31, 1994," the judge wrote in the warrant request.

France grants immunity to acting heads of state, preventing judicial authorities from issuing a warrant for Mr Kagame, who the judge has asked to be tried by a UN court instead. Those targeted include James Kabarebe, armed forces chief, and Charles Kayonga, army chief of staff.

Warrants also were issued for those suspected by Mr Bruguiere of actually attacking the plane - Franck Nziza, believed to be a captain in the presidential guard, and Eric Hakizimana, of the secret service.

Mr Kagame has lashed out at the judge and his claims, calling him "an imposter, a politician" in an interview. He also promised that ties between the two nations would suffer.

France annulled Rwanda’s entire $45 million bilateral debt this year but the action has done little to improve relations between the two, which have been strained for years over the genocide. Mr Kagame has accused France of doing too little to stop the slaughter.

France’s Foreign Ministry said it would maintain its ambassador in Rwanda despite the recall. "We believe it is very useful to keep open all the lines of dialogue with Rwandan authorities," spokesman Jean-Baptiste Mattei said. He insisted that France had put no political pressure on the judge in making his decision.

Rwanda has appointed a commission to determine if there is evidence to prosecute France for damages. The panel began open hearings last month and is set to resume these on December 11.

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