Special judge SR Tamboli allowed the plea moved by the CBI prosecutor A Limosine in this regard.
Mr Limosine told the court that the agency had sent three summons to Choksi on his email id, however, he has neither responded to them nor appeared before the agency.
The prosecution said there was "every reason to believe" that Choksi had fled the country and is in hiding, and that steps are being taken to secure his presence by issuance of red corner notice by the Interpol.
"...to secure his presence and to pursue the same, an open non-bailable warrant is required against Choksi," Mr Limosine told the court.
It is alleged that the LoUs (Letter of Undertaking) and LCs (Letter of Credit) worth close to USD 2 billion were issued to the companies of accused Choksi and his nephew Nirav Modi from the Brady Road branch of the PNB in Mumbai through SWIFT (Society for Worldwide Interbank Financial Telecommunication) messages.
These messages were allegedly not entered in the banking software of the PNB to bypass surveillance.
Several bank employees have been booked for collusion in the case.
The CBI court had last week issued a non-bailable warrant against Nirav Modi.
Both Choksi and Nirav Modi have been booked in two cases each related to the bank fraud under the Prevention of Money Laundering Act and the Indian Penal Code.
The duo reportedly left the country in the first week of January this year, days before the alleged fraud came to light.
The CBI had approached the Interpol with a request for issuing a 'Diffusion Notice' which was aimed at locating an individual.
The agency has arrested 19 people so far in connection with the fraud. The Enforcement Directorate (ED) is also conducting an independent probe.
The Central government has claimed to have tracked Modi in Hong Kong and sought his arrest under the 'Surrender of Fugitive Offenders Agreement' with Hong Kong.