A division bench of Justices V M Kanade and M S Sonak directed the CBFC to consider whether guidelines of the Cinematograph Act were followed before granting certification to Bhansali's movie.
"Although the board has said that the guidelines were followed in our view there has been non-application of mind," the court said.
The CBFC shall also see if any content of the movie or its title has violated any fundamental rights of citizens.
Shukla in his petition had claimed that the film's title is misleading and the contents have hurt the religious sentiments of Lord Ram and Hanuman followers.
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The CBFC has been directed to hear the petitioner and pass an order within four weeks.
The bench also noted that the CBFC has to be careful in future while issuing certification to movies.