Htin Kyaw was tapped earlier this year to become the country's first civilian leader in decades by Aung San Suu Kyi, the veteran democracy activist who still controls the administration but is barred from the presidency by a junta- era charter.
Her National League for Democracy (NLD), which is packed full of former political prisoners jailed for their activism under military rule, ended nearly half a century of army domination when they took power in a historic transition in March.
The pardon was intended to "make people feel happy and peaceful, and (promote) national reconciliation during the New Year", it added.
Suu Kyi, who spent some 15 years under house arrest, pledged in a statement earlier this month to make releasing prisoners of conscience a priority of her administration.
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Since the NLD took power, authorities have dropped charges against nearly 200 political activists, according to police, including dozens of students who spent more than a year in jail over an education protest.
"We are trying to set the political prisoners, political activists and the students who face trials concerned with politics free," the president said in his first lengthy public address since taking office.
Htin Kyaw was little known outside his home country before taking office, but is a longtime friend and close aide of Suu Kyi.
Despite being blocked from the presidency, she wields formal power over the government through her newly-fashioned role as state counsellor, which the NLD created for Suu Kyi through their hefty majority in parliament. She has also taken on several cabinet posts, including foreign minister.
Watchdog groups in Myanmar say there are still hundreds of activists facing trial or being held in the country's notorious prisons, many of them arrested under the quasi- civilian government that stepped down last month after five years of transitioning the country from junta rule.
Myanmar's new year holiday, a Buddhist celebration known as Thingyan, falls in mid April and sees most offices close while people line the streets to douse each other with water to wash off the past year's sins.