A local court in Anantapur issued the arrest warrant as Dhoni did not appear in the court despite three summons served in the past. It directed police to present Dhoni in the court on July 16.
The case relates to a picture on the cover of a magazine.
Business Today in its April 2013 edition had carried the picture. Dhoni was portrayed as Hindu god Vishnu with a subtitle "God of Big Deals" and holding products of several companies including a shoe in his hand.
Y Shyam Sunder, a local leader of the Vishwa Hindu Parishad (VHP), had filed a petition in the court in February this year alleging that the cricketer hurt the sentiments of Hindus by denigrating a Hindu god.
The summons issued by the court to Dhoni on three occasions were returned. The court, which took up the hearing Tuesday, issued the arrest warrant.
Similar petitions against Dhoni were filed in Delhi, Pune and other cities.