Over 700,000 of the beleaguered minority have fled to neighbouring Bangladesh since August past year after a Rohingya militant attack in Rakhine state triggered a scorched earth military campaign there.
Speaking at the World Economic Forum in Hanoi on Thursday, Suu Kyi said the army's brutal crackdown on the Muslim minority - described by the United Nations as "genocide" - "could have been handled better".
"For the government, we have to be fair to all of them, even if the rest of the world is not interested", Aung San Suu Kyi said on Thursday.
"The judgment ... had nothing to do with freedom of expression at all", Myanmar State Counsellor Aung San Suu Kyi said on Thursday at the regional forum in the Vietnamese capital Hanoi.
However, Aung San Suu Kyi said the reporters have the right to "appeal the judgment and to point out why the judgment was wrong".
Wa Lone, 32, and Kyaw Soe Oo, 28, were each imprisoned for 7 years last week for breaching the country's hardline Official Secrets Act while reporting on atrocities committed during the military crackdown in Rakhine state.
Suu Kyi's speech would seem to indicate the worldwide condemnation on both cases has finally gotten through to former Nobel Peace Prize victor.
The violence in Rakhine has eased but Myanmar now has to deal with its aftermath, especially the repatriation of the Rohingyas. "We can't choose who should be protected by rule of law", she said in rare comments on the crackdown.
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There have been calls to strip Ms Suu Kyi of her Nobel Peace Prize which she received in 1991 for her work to "establish a democratic society in which the country's ethnic groups would cooperate in harmony".
Myanmar government leader Aung San Suu Kyi will not attend the U.N. General Assembly in NY next week, media reported on Wednesday, amid growing calls for Myanmar's security forces to be held accountable for alleged crimes against Rohingya Muslims. "We can not choose and pick".
The pair has denied the charges, insisting they were set up while exposing the extrajudicial killing of 10 Rohingya Muslims in the village of Inn Din in September past year.
They were sentenced to seven years in prison on September 3 for violating the state secrets act.
When asked to comment on Pence's call to release the journalists, the Myanmar leader responded by asking if the critics felt there had been a miscarriage of justice.
Aid workers have also said it is not safe for refugees to return yet.
'Sentence has been passed on them because the court has decided they had broken the Official Secrets Act'.
"We just have to makes sure that we make enough progress between now and then for the people to decide that they can safely continue to give us the responsibility to look after our country", she said. "On all these counts, the trial of the Reuters journalists failed the test".