The Indian Performing Rights Society (IPRS) represents composers, lyricists, music producers and the publishers of music and issues licenses permitting usage of that's registered within India.
The FIR mentions names of YRF Company and its directors Aidtya and Uday Chopra, an official said.
The complainant claimed the IPRS has the exclusive right to collect royalties on behalf of artists and music producers but the YRF collected it unauthorisedly.
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"Yash Raj Films Company and its directors allegedly pocketed Rs 100 crore by collecting music royalties of members of the Indian Performing Rights Society (IPRS)," the official said quoting the complaint.
The case has been registered under sections 409 (criminal breach of trust) and 34 (common intention) of the Indian Penal Code (IPC) and relevant sections of the Copyright Act, the official said.
"Since this is a legal case the board cant comment about it until tomorrow," said a representative of the IPRS.
The YRF has so far not issued a statement.
(With additional information from PTI)