Zaw Htay, director of the president's office, said on Twitter that the amnesty showed Thein Sein's determination to have an "inclusive political process," denying that the dissidents were being used as political tools.
Thein Sein, a former general, has freed hundreds of political detainees since coming to power in early 2011 as part of sweeping changes that have led to the end of most Western sanctions.
But activists say some 200 political prisoners remain in jail and accuse Myanmar of using a series of headline-grabbing amnesties for political gain.
Opposition member Nay Myo Zin, whose previous amnesty was revoked earlier this month to the dismay of campaigners, was among those freed on Friday.
"I was invited to cooperate with the authorities in this reform process," he told AFP by telephone after his release from prison in the Irrawaddy region.
"We have a good foundation for the reform process. We have moved on from the old era," he added.
Thein Sein, who will be welcomed at the White House on Monday, will be the first leader of the former military-ruled nation to visit Washington since 1966.
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