The FIR was registered in Nagpada police station against the owner, editor, writer and cartoonist of the newspaper, said senior police inspector Shivaji Kadam.
The Marathi language newspaper allegedly published some words embedded in a graphic design in its write-up that appeared in today's pullout.
A case has been registered under sections 153-A (punishment to persons who indulge in wanton vilification or attacks), 295-A (deliberate and malicious acts, intended to outrage religious feelings of any class by insulting its religion or religious beliefs) and other sections of IPC, Kadam said.
Meanwhile, the newspaper has published an unconditional apology and posted it on its online edition.