The Assistance Association for Political Prisoners said those pardoned included two peace activists jailed for leading a peace march to troubled Kachin state, Voice of America reported.
Despite Thein Sein's promise in July to release all political prisoners by the end of 2013, AAPP advocate Bo Kyi said about 40 prisoners still had not been freed under the amnesty.
Another 200 prisoners facing trial should have their charges dropped, Bo said.
Bo said the rest of the prisoners should be released during the first week of January.
Some 41 activists were released earlier month in conjunction with the Southeast Asia Games held in Myanmar's capital, Naypyidaw. AAPP said two were re-arrested within days.
Since becoming president in March 2011, Thein Sein has released about 1,300 political prisoners.