The fraud which began in March 2011, is now estimated to have crossed $2 billion (about Rs 13,000 crore).
PNB had previously pegged its exposure to the Gitanjali companies at Rs 6,138 crore.
Tuesday's disclosure takes PNB's overall exposure in the still unravelling fraud case to well over the $2 billion mark.
Lenders will have to look at alternative instruments like bank guarantees.
India's central bank for the first time scrapped the system of issuance of guarantees like Letters of Undertaking (LOU) and Letters of Comfort (LOC) in the wake of the biggest-ever bank fraud of 1.8 billion US dollars. "This is clearly a risk mitigating step as letter of credit are governed by Uniform Customs and Practice for Documentary Credits, which has a well defined set of rules and procedures", said a senior official at one of the public sector banks. It will also put companies that have received credit based on LoUs in a spot, as they have to now repay their borrowings since there will no rollover of existing LoUs.
RBI also barred lenders from issuing letters of comfort (LoC) as trade credit for importing goods into India with immediate effect.More news: 'Queer Eye' contestant Tom Jackson gets engaged to ex-wife Abby
The buyer's credit usually goes to an overseas nostro account from where the payment to the importer's bank is made.
Two more Delhi-based industrialists have duped Bank of Baroda of Rs.6000 crores, it has been reported. "A LoU does not have these details and when it is not linked to the banking system it can not be traced, like it happened with PNB". Such transactions went on for six years without detection.
Though Modi has not yet been arrested, India's External Affairs Ministry has revoked his passport as well as Choksi's for their involvement in the scam. The investigating agency further submitted that there is a shortage of officers of the rank of inspectors and above in the CBI Bank Securities and Fraud Cell.
Both Modi and Choksi are overseas and have refused to return to face trial.
LoUs and LoCs are used widely in several industries including gems and jewellery, oil and gas, electronic goods, solar panels and metals.
PNB did not immediately respond to requests for comment.