The Federal Capital Territory (FCT) Police Command has arraigned 38 members of the Shiite Islamic Movement of Nigeria (IMN) in various courts in Abuja.
Ten members of the sect were brought before a magistrate court in Wuse Zone 2.
Twenty eight others were arraigned at a Magistrate court in Wuse Zone 6.
The defendants, who could not understand English, with the help of an interpreter, pleaded not guilty to the charges preferred against them.
The charges border on criminal conspiracy, unlawful assembly, assault and others.
Following this, the counsel to the defendants, I.A Ishaq, moved a motion praying that his clients be released on bail.
Mr Ishaq also drew the courts attention to the fact that nine of the defendants are minors.
Prior to this, the judge, Raphael Joshua, ordered that the minors be “remanded in a decent facility outside the police cell”.
The judge then adjourned the case to July 18 to rule on the bail application.
The police had on Tuesday said two of its officers were shot by suspected members of the Shiite IMN.
This, the force said led to the arrest of 40 protesters.
The Shiites are demanding the release of their leader, Ibrahim El-Zakzaky, who has been detained by the government since December 2015.
Over 340 Shiites were reportedly killed by the army in December 2015 after the army accused the Islamic sect of blocking their path.
No army officer has been arraigned.