In one district, civil society leader Dieudonne Bashirahishize led more than a thousand protesters to observe a minute of silence "for the martyrs of the fight for freedom", calling on people to "overcome our fear and continue to demonstrate despite threats".
At least 20 people died in weeks of street battles with security forces before demonstrations ended last week when generals launched a failed coup attempt, but protests resumed again yesterday.
Opposition and rights groups say that Nkurunziza's bid for a third five-year term in power is against the constitution and the terms of the peace deal that brought an end to the country's 13-year civil war in 2006.
"We cannot stop the protests, because President Nkurunziza has not withdrawn his candidacy," said Bernard, a 34-year old unemployed man..
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Groups scattered as troops fired warning shots, gathering again elsewhere to resume protest chants. Several protesters were seen who appeared to have been beaten, with swollen or bloody faces.
"We started before them, and they are now in prison," Banvugiyuvira told the crowds. "We have just shown that Burundians can fight for their rights. We refuse to be slaves of Nkurunziza ... We continue our struggle! If Nkurunziza wants us to leave the streets, he must renounce his third term."
Nkurunziza, a former rebel leader and born-again Christian who believes he has divine backing to lead the country, argues his first term in power did not count as he was elected by parliament, not directly by the people.
But the presidency dismissed such claims Tuesday, saying it would never carry out "revenge" raids and promising fair trials for those arrested.