The case has been filed by producer Shakeel Noorani who has alleged that he received threat calls from underworld at Dutt's behest.
Acting on Noorani's complaint, a Metropolitan court in suburban Andheri had on February 13 this year asked Dutt to appear before it to answer allegation of criminal intimidation levelled against him by the producer.
As Dutt failed to appear twice in this case in response to summonses issued against him, the court today issued a non-bailable warrant against him on a plea made by Noorani, the producer's lawyer Neeraj Gupta said.
Dutt was not available for comment. However, his lawyer Rizwan Merchant had earlier denied that threat calls were made at the actor's behest and said they would present their case in the court.
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Noorani had earlier approached Indian Motion Picture Producers' Association, which had directed Dutt to pay Rs 2 crore to Noorani for the loss incurred during the shooting.
As the filmstar did not pay the money, Noorani approached the Bombay High Court and prayed for execution of the order passed by IMPPA. In 2010, the High Court had ordered attachment of two properties of the 53-year-old actor.
Dutt's lawyer had refuted allegations that the calls had been made at his client's behest and claimed he had been falsely implicated. Merchant said calls were made in 2011 and Noorani may have "engineered" the calls after visiting Pakistan.
Dutt, was last month ordered by the Supreme Court to go back to jail and serve three-and-a-half-years of remaining sentence in the 1993 Mumbai serial blasts case. He was last week given four weeks to surrender and undergo the sentence.