A top suspect accused of forming secret death squads and orchestrating the killings of thousands during Rwanda's 1994 genocide pleaded not guilty on Wednesday to war crimes charges.

Idelphonse Nizeyimana, Rwanda's former deputy intelligence chief, entered his plea at the International Criminal Tribunal for Rwanda after being captured in Uganda earlier this month.

"I am not guilty," Nizeyimana, 46, said each time the four counts of war crimes charges was read out to him. A trial date will be set later.

Nizeyimana is accused of ordering the killing of children, hospital patients, priests and even an elderly and revered African queen.

More than 500,000 members of the Tutsi ethnic minority and moderates from the Hutu majority were slaughtered during the 100-day Rwandan genocide in 1994.

Until his capture, Nizeyimana had been on the run for 15 years with a bounty on his head. He was believed to have hidden in the jungles of eastern Congo, where he belonged to a Rwandan Hutu militia called the Democratic Forces for the Liberation of Rwanda that continues to commit atrocities.