"There are still many prisoners who we expected to be released and who the people expected to be released. We feel frustrated," Nyan Win, spokesman for Aung San Suu Kyi's National League for Democracy party, told AFP.
The regime pardoned more than 200 political detainees, according to Thailand-based Assistance Association for Political Prisoners (AAPP), but kept most of its roughly 2,000 political detainees -- including democracy campaigners, journalists, monks and lawyers -- locked up.
Activists have criticised the new nominally-civilian government for not freeing more political inmates on Wednesday in its amnesty for more than 6,300 prisoners.
The prominent satirist and vocal government critic Zarganar, who goes by one name, was among those released and AAPP said the regime also freed General Hso Ten, a prominent ethnic Shan leader sentenced to 106 years for charges including high treason.
But it said many leading dissidents, including key figures involved in a failed 1988 student-led uprising, remained locked up.
AAPP said the final figure for the number of dissidents freed has yet to be confirmed -- partly because the government does not explicitly recognise political prisoners.
A prison official told AFP that all those included in Wednesday's pardon had already walked free.
"The amnesty is finished. All prisoners on the list were released yesterday," he said.
Myanmar's new government, led by former general President Thein Sein, has appeared keen to burnish its image and has raised hopes of reform by reaching out to critics including pro-democracy leader Suu Kyi.
The fate of political prisoners in Myanmar is a key concern of western governments that have imposed sanctions on the isolated nation and its leadership.
Many political prisoners were sentenced to decades in jail and have endured "torture and other forms of cruel, inhuman or degrading treatment", according to Amnesty International, which urged the regime to go further.