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Zakzaky has been in custody since December 2015 despite court orders that he should be freed
Scores of protesters were also arrested by armed police wearing bulletproof vests and gas masks during clashes in Abuja, the national capital.
“We’ve come under serious attack today,” said Deji Adeyanju of Concerned Nigerians, a civil society group involved in the demonstration.
“The more they attack the more (we) come out,” Deji said. “We want to defy tyranny and a dictatorship.”
The police did not immediately comment.
Zakzaky, head of the Islamic Movement of Nigeria (IMN), has been in government custody since troops clashed with his followers in the northern city of Zaria in December 2015 despite court orders that he should be freed.
More than 350 IMN followers were killed in the 2015 clashes. Zakzaky was shot and injured leaving him partly paralysed and blind in one eye.
The Shiite leader has repeatedly been imprisoned for alleged incitement and subversion.
IMN has been in conflict with the Nigerian government for years, seeking to foment an Iranian-style Islamic revolution in the country’s Sunni Muslim-majority north.
Zakzaky’s followers on Monday had clashed with the police in Abuja’s Maitama area and police made at least 115 arrests.
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