The court ordered that they be remanded at the Afara Federal Prisons in Aba.
The suspects were arraigned for alleged conspiracy, terrorism, attempted murder and membership of unlawful society.
Counsel to the suspects challenged the jurisdiction of the court even as the case was adjourned to October 25.
The detained IPOB members were among those arrested in the clashes with security officials which led to the death of a police officer and burning down of a police station.
The secessionist group was subsequently declared a terrorist organisation by the military authorities.
The IPOB group was proscribed by the Southeast governors as well as River state government even as the federal high court also declared it a terrorist organisation.
The leader of IPOB, Nnamdi Kanu is currently facing treason charge, for which he is on bail.
