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A first group of 300 were released from the Mpimba central prison in Bujumbura, but authorities aim to free some 2,500 of the total, which stood at 10,051 last month.
The releases, which included 58 activists arrested in a police crackdown on demonstrators in April 2014, were aimed at “relieving prisons to allow those remaining to live in acceptable conditions,” said Justice Minister Aimee Laurentine Kanyana.
“Every time political prisoners are released it’s a good thing,” Pierre-Claver Mbonimpa of the Aprodeh prisoners’ defence group told AFP.
“But we are calling above all for the release of over 4,000 political detainees since the start of the crisis in Burundi,” added Mbonimpa, who lives in exile in Belgium.
But he said the pardon by President Pierre Nkurunziza was also aimed at “making space for the victims of numerous arbitrary arrests which add to the repression which Burundi suffers”.
Burundi has always denied holding political prisoners.
The African country has been in the throes of a serious, sometimes deadly political crisis since April 2015 when Nkurunziza announced his intention to run for a third term which opponents said was unconstitutional.
He went on to win an election in July that was boycotted by the opposition and criticised by outside observers.
The violence in Burundi has so far killed at least 500 people and driven more than 300,000 to leave the country.
Burundi has also moved to quit the International Criminal Court which was investigating the country, and cut ties with the UN’s main human rights body after a damning September report detailed atrocities and warned of “genocide”.