The case had been brought by a member of the Hindu nationalist movement, who said the publication of the picture in 2013 had hurt religious sentiment.
A drawing appeared on the front of Business Today in April 2013 showing the 34-year-old as a Hindu deity.
The wicketkeeper/batsman had now been asked to appear at a court in Anantapur.
The non-bailable warrant was a result of a petition filed by local Vishwa Hindu Parishad leader Shyam Sunder, who said the picture "hurt Hindu sentiments".
Dhoni's lawyer said the warrant was "erroneous" and denied receiving any summons.
The cricketer's management added that the player had nothing to do with the picture, which went with the headline "god of big deals".
"Neither did he pose for the picture, nor were we aware of such a picture being published," Rhiti Sports' Arun Pandey told ESPNcricinfo.
The summons has been scheduled for 25 February, a week before the World T20 tournament begins in India.