The meeting was the first such contact with Myanmar's military dictators in nearly two years, and she is believed to have offered to help the government get international sanctions against the country lifted.
She met Aung Kyi, a retired major general who is also the regime's labor minister, for nearly an hour at a government guesthouse near her lakeside home in which she is serving another house detention.
It was the first time the two have met since January 2008, according to a report on the Irrawaddy news Web site.
"The meeting started at 1 pm and lasted about 45 minutes," said Nyan Win, Suu Kyi's lawyer and a spokesperson for her banned National League for Democracy party.
Suu Kyi sent a letter to the country's military leader, Senior Gen. Than Shwe, on Sept. 25 offering to cooperate with the junta to lift sanctions against the country, formerly called Burma. She also asked to meet with envoys from the United States, the European Union and Australia to learn more about the sanctions, said Win.
The two had met previously on several occasions after the regime's 2007 crackdown on Buddhist monk-led mass demonstrations, an issue that remains a flashpoint for the military rulers.
Police and armed forces in the city of Yangon, formerly Rangoon, are on alert this week to prevent protests by monks demanding an apology from the junta for the September 2007 crackdown.
The All Burma Monks' Alliance wants the regime to apologize for the violent suppression of the peaceful 2007 demonstration in the city of Pakokku. The alliance also wants the release of all monks imprisoned since the so-called Saffron Revolution, the movement that has grown out of the Pakokku demonstrations.
Suu Kyi, 64, was the winner of the country's 1990 general election, which the generals refused to recognize. She has since spent 14 of the past 19 years under some form of imprisonment including house arrest.
Last week Suu Kyi, a Nobel Peace Prize laureate, lost her appeal against her 18 months of house arrest that was handed down in a surprise move by the country's highest court in early August.
She faced up to five years in jail for breaking the terms of her previous house arrest after U.S. citizen John Yettaw swam across a lake and entered her home uninvited. He stayed for two days despite efforts by Suu Kyi and her two female aids to persuade him to leave.
Suu Kyi was initially given a sentence of three years in jail with hard labor, but this was immediately commuted to another house detention. Yettaw, although sentenced to seven years hard labor, has since been released back to the United States.
Also last week, Myanmar's traditional allies China, India and Russia joined an international call for Myanmar to release all political prisoners including Suu Kyi and allow them to take part in next year's elections.
The Geneva-based U.N. Human Rights Council's 47 members unanimously adopted the resolution.
Suu Kyi is the leader of the League for Democracy Party. But her current house detention sentence, while appearing lenient, likely means she is not eligible to be a candidate the election that the generals plan for 2010.
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