Hundreds of thousands of Rohingya were forced to flee Rakhine into neighboring Bangladesh following a violent government crackdown in August past year, precipitating one of Asia's worst refugee crisis.
"We have to be fair to all sides", Aung San Suu Kyi said.
In just under three years, Myanmar's 1991 Nobel Prize Laureate, Aung San Suu Kyi has gone from triumphant former political prisoner - feted around the globe as Southeast Asia's Nelson Mandela - to her country's de-facto leader (or is she?) and a spectacular disappointment to those same supporters.
"The judgement ... had nothing to do with freedom of expression at all, it had to do with the Official Secrets Act", she said.
But she added that the two journalists "have every right to appeal the judgement and point out why the judgement is wrong if they consider it wrong".
The journalists, Wa Lone, 32, and Kyaw Soe Oo, 28, were found guilty on official secrets charges and sentenced earlier this month in a landmark case seen as a test of progress towards democracy in Myanmar.
Nobel Peace Prize victor Suu Kyi heads the civilian government in the specially created role of state counsellor, but also serves as minister of foreign affairs.
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Bangladesh and Myanmar reached a deal in November to begin repatriation within two months, but it has not started, with stateless Rohingya still crossing the border.
Daw Aung San Suu Kyi defended a Yangon court's decision to jail two Reuters reporters and admitted the Rakhine crisis "could have been handled better" in an onstage interview at the World Economic Forum on ASEAN that also addressed investment and the potential for constitutional change. "We can not choose and pick".
"They were not jailed because they were journalists".
Asked by Mr Brende about the case of the Reuters journalists, she replied: "If anybody feels there has been a miscarriage of justice I would like them to point it out".
In the camps in Bangladesh, which constitute the world's largest single refugee settlement, some Rohingya have expressed reluctance to return to the site of so much slaughter by the Myanmar military and Buddhist mobs.
The two news agency journalists were arrested while carrying official documents given to them by police officers while investigating a massacre of ten Rohingya men by the military at Inn Din in the Rakhine state. Seven Burmese soldiers have since been sentenced to ten years of hard labour for their role in the crime.
Earlier Suu Kyi, Myanmar's de facto leader, hit back at widespread worldwide concern over the trial, challenging critics to show where there had been a miscarriage of justice and insisting they had been fairly tried "in open court".