In its complaint, Prernaa's banner had accused John and his company of cheating, breach of trust, fraud, misappropriation of funds and copyright infringement.
KriArj Entertainment alleged that they have been duped of crores of rupees which they had invested in 'Parmanu'.
The FIR has been filed at the Khar police station in Mumbai.
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On March 31, JA Entertainment said in a statement that it has terminated the 'Parmanu' contract with KriArj owing to non-payment of dues and multiple postponements of film's release.
KriArj then went on dub John's notice as 'false and illegal'.
Later, John's company released a fresh statement countering the claims by Prernaa's banner.
As of now, the release date of 'Parmanu' has been fixed as May 4.
If there isn't any further delay, it will be clashing with Amitabh Bachchan and Rishi Kapoor starrer '102 Not Out'.
Also starring Diana Penty, the film was initially scheduled to release on December 8 last year.
'Parmanu' is based on India's nuclear tests in Pokhran.