The warrant was issued by the Judicial Magistrate First Class (JMFC), Narendra Jain on a petition filed by the Convenor of the orgnisation `Tiranga Abhiyan', Ravi Atrolia.
Earlier the court had issued bailable warrants against Dutta in the case, but he had obtained a stay from the High Court.
However, the High Court had later dismissed his application.
Following dismissal, Dutta was supposed to appear in the court today but, he failed to do so following which arrest warrant was issued against him, Abhiyan's lawyer, Shailedra Dwivedi told reporters.
The Abhiyan alleged in its complaint under Prevention of Insult to the National Honour Act, that in the film Dutta had wrongly displayed the national flag over the coffin of the soldiers, thereby insulting the tricolour.
The court has fixed May 24 as the next date of hearing in the case, Dwivedi added.