The court of Dhaka Metropolitan Magistrate Shahriar Mahmud Adnan issued the warrant on Wednesday after Siddique failed to appear before it.
It had earlier summoned him in the case filed on Oct 2 by lawyer Shah Alam.
Siddique drew widespread condemnation after rubbishing the practice of Hajj and Tabligh Jamaat at a programme in New York on Sept 28.
A video clip of his utterances kicked up a storm as it went viral on the internet.
“So much manpower is wasted over the Hajj. Two million people are now in Saudi Arabia for the Hajj. They have no work or role in production. They only eat and go abroad using the country’s money,” Siddique was heard saying in the video.
Since then, over two dozen cases have been filed against him at different courts in several districts of Bangladesh, accusing him of hurting religious sentiments.
Amid the furore, the government dropped him from the Cabinet while the Awami League expelled him from the policy making Presidium on Sunday.
On Tuesday, the party showcaused him seeking explanation on why his party membership would not be cancelled.
Now in Kolkata, Siddique told bdnews24.com on Tuesday he will reply to the show-cause "as and when I get it and within the time limit mentioned".