The court, set up under the Prevention of Money Laundering Act, issued the non-bailable warrants on applications filed by the Enforcement Directorate, one of the agencies probing the bank fraud cases registered last month.
The ED had earlier issued summonses to Mr Modi and Mr Choksi, both key accused in the scam cases, asking them to appear before the central agency.
However, the two diamond traders, who are said to have left the country before criminal cases were registered, had failed to appear before the ED. The agency then moved the court for issuance of non-bailable warrants against them.
On February 27, the ED had moved the court seeking a non-bailable warrant against Mr Modi.
The agency had told the court that it had issued three summonses to Mr Modi to appear before it.
"We issued three summonses to (Mehul) Choksi. He neither responded to those summonses nor appeared before the agency," special ED prosecutor Hiten Venegaonkar had told the special court presided over by Judge MS Azmi on March 1.