The Ministry of Information announced the amnesty on its website on Tuesday, saying the prisoners were being freed "on humanitarian grounds".
It did not refer specifically to political prisoners, and most of those released had committed minor crimes.
The Political Prisoner Scrutiny Committee said that at least 13 of those pardoned were jailed on political offences and at least eight were former senior military intelligence officers detained after the 2004 ousting of former prime minister and intelligence chief, Khin Nyunt.
The family of at least one former senior military officer confirmed the release, Al Jazeera reported.
General Thein Swe, arrested in a 2004 purge on his department during junta rule - was among those freed.
"Having a top day with great news. I'm heading to Myingyan to pick up my dad," said Sonny Swe, the general's son and a well known media businessman, on social media.
Ye Aung, a former prisoner himself and now a member of the government committee, said the amnesty appeared to have been timed ahead of a meeting of Asia-Pacific leaders in Myanmar next month.