An Abuja high court on Thursday ordered the release of Nnamdi Kanu, which prompted celebrations on the streets.
The police in Onitsha city said shots were fired after officers were attacked and three people were "feared dead".
Mr Kanu was arrested by the authorities in October, accused of treason.
He is the director of the banned Radio Biafra and heads the separatist Indigenous People of Biafra (IPOB) group.
Biafran secessionists fought a three-year civil war in which more than one million people lost their lives. The uprising was eventually quelled by the military in 1970.
The court order to free Mr Kanu came after Nigeria's secret police withdrew criminal charges against him. It is not clear what these were, but may have been related to running a radio station without a licence.
But he has not been released from detention as the police say they are still investigating his alleged involvement in terrorist activities.
'Officer severely injured'
The clashes in Onitsha were prompted by "overzealous police officers firing at unarmed civilians who were celebrating a court victory", IPOB co-ordinator Uchemna Madu told the BBC Hausa service.
Fifteen other people were seriously wounded, he said.
A Pro Biafra protester in southern Nigeria on Sunday 8 November, 2015
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