But she said that Myanmar was undertaking its own investigations, adding: "Surely under the circumstances, genocidal intent can not be the only hypothesis".
Numerous restrictions, including those on citizenship rights, freedom of movement, and access to education and healthcare, continue to be placed upon the Rohingya in Myanmar.
Once hailed worldwide as a rights icon for her defiance of the same generals she is now defending, Suu Kyi also warned the Hague-based court that its involvement in the case risked "feeding the flames of extreme polarisation".
Ms. Suu Kyi was testifying in defence of her country, which is facing charges of genocide committed against the mainly-Muslim Rohingya minority group, brought by The Gambia, on behalf of the Organization of Islamic Cooperation.
Suu Kyi, however, said that the court, set up in 1946 to rule on disputes between member states, had not confirmed genocide in cases of mass expulsions of civilians in the 1990s Balkans war.
The Gambia meanwhile enjoys the support of the 57-member Organisation of Islamic Co-operation (OIC) and a team of global lawyers to push the case although the ICJ itself has no way of enforcing the outcome - and neither Aung San Suu Kyi nor the generals would automatically be arrested and put on trial.
The Rohingya garner little sympathy within Myanmar, where many people buy the official line that the minority are illegal immigrants from Bangladesh, even though many trace their roots back generations. Her win in Myanmar's first-ever democratic elections three years ago was celebrated worldwide.
"Please bear in mind this complex situation and the challenge to sovereignty and security in our country when you are assessing the intent of those who attempted to deal with the rebellion", she said.
Suu Kyi said claims made the previous day at the ICJ by Gambia, which submitted the lawsuit against Buddhist-majority Myanmar on November 11 with support from the Organization of Islamic Cooperation, were "incomplete" and "misleading".
The Rohingya have faced decades of persecution at the hands of the Myanmar military, but never on this scale.
Suu Kyi, once feted in the West as a heroine of democracy, spoke for about 30 minutes at the courtroom in The Hague in defense of the actions of the Myanmar military that for years had kept her under house arrest. She attributed the exodus of more than 740,000 civilians to neighboring Bangladesh to an ongoing internal armed conflict with insurgents.
The Gambia, which is mostly Muslim, accuses Myanmar of breaching the 1948 genocide convention and has asked the court to take emergency measures to stop further violence.
On Wednesday, some refugees shouted "liar, liar, shame!", as they watched Suu Kyi defend Myanmar's case on television.
She was awarded the 1991 Nobel Peace Prize in absentia for championing democracy and rights under Burma's then-ruling junta.
Political analyst Maung Maung Soe defended Aung San Suu Kyi's testimony, saying that she can not effectively prosecute offenders under a constitution that gives the military huge power.
Myanmar's civilian leader and Nobel peace laureate Aung San Suu Kyi admitted during the ICJ hearing that the army may have used "disproportionate force" but said that did not prove it was trying to wipe out the Rohingya Muslims in Rakhine state.
"When I looked into the eyes of those refugees as they recounted their devastating stories, I could see the looks of fear, of despair, of desperation, and of destruction", he told the court. As reports of ethnic cleansing emerged, the world reacted with disbelief as Suu Kyi stayed silent. She also knows that people in Myanmar do not like seeing their country publicly attacked by foreigners.
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