Officials told The Express Tribune that the cases had been filed in which a total of 218 people were nominated.
Hundreds of angry protesters took to the streets in Ghotki on Sunday after Notan Lal, a member of the Hindu community and principal of the Sindh Public School, was accused of passing "blasphemous remarks" by a student.
Additional Inspector-General for Sukkur Jamil Ahmed said an FIR was filed against the principal on the complaint of Abdul Aziz Rajput, the student's father who claimed that the teacher had committed blasphemy by making derogatory remarks against Prophet Muhammad.
Lal was booked and arrested following the protests, road blockages and riots in Ghotki city and its adjacent small towns.
The mob also vandalized the Sacho Satram Das temple and five shops owned by members of the Hindu community in Ghotki's Jilani Market, besides a private school were set alight.
In the first case registered against the rioters, 45 people were booked under Section 295 of the Pakistan Penal Code (injuring or defiling place of worship, with intent to insult the religion of any class).
Of these 45, officials said, 22 people were identified, while 23 remain unidentified.
In the second case, 150 people - 27 identified and 123 unidentified - were accused of blocking roads and disrupting vehicular traffic.
A total of 23 people - 12 identified and 11 unidentified - were nominated in the third case which pertained to ransacking and damage to property.
Ahmed said all three cases were registered on behalf of the state. "This is a warning to all such miscreants that no one will be allowed to challenge the writ of the state."
( With inputs from IANS )