The warrant was issued after the National Investigation Agency or NIA informed the court that Mr Naik had failed to respond to three summons in cases filed under Unlawful Activities (Prevention) Act against him last year.
The NIA will need to seek the help of Interpol to bring Mr Naik back to India from abroad, the agency said.
This is the second non-bailable warrant or NBW against the 51-year-old after the Special Prevention of Money Laundering Act Court issued an NBW last week in a money-laundering case filed by the Enforcement Directorate, after he failed to appear before it.
Following the Dhaka terror attacks last year, the NIA had filed the case against Mr Naik and other officials of his Mumbai-based NGO Islamic Research Foundation (IRF).
Mr Naik was on a tour abroad at that time and has since not returned to India allegedly to evade arrest under various charges, including inspiring terrorist activities and money-laundering.
In December last, the centre had permanently cancelled the Foreign Contribution (regulation) Act or FCRA licence of Mr Naik's NGO and his educational trust after declaring it as a terror outfit.