On a complaint by lawyer Karuna Sagar, a case was filed against Varma at the Saroornagar police station in Cyberabad.
"We have registered a case against Varma. We will seek legal opinion before proceeding further in the case," Saroornagar police inspector B. Naveen Reddy told IANS.
The filmmaker was booked under four sections of the Indian Penal Code - sections 153 A (promoting enmity between different groups), 504 (intentional insult with intent to provoke breach of peace), 505 (statements conducing to public mischief), and 298 (hurting religious feelings).
The complainant alleged that Varma hurt the religious sentiments of Hindus by insulting Lord Ganesh through his series of tweets.
Several police complaints were also filed against Varma in Mumbai for his objectionable remarks on Lord Ganesh, though he apologized for these later.
On Aug 28, a day before the 11-day Ganeshotsav began in Mumbai, Hyderabad and other places, the filmmaker posted a series of tweets about Lord Ganesh.
The next day, he gave a clarification, saying they were made in a usual manner.
"All tweets I put on Ganesha were in my usual manner but unintended by me to hurt anyone's sentiments... but if they did I sincerely apologise," he tweeted Saturday.