Khan added India did not have much in payments left to be made to Iran, and declined to be pinned down to a specific figure.
"Not much is going to be paid," Khan told reporters on the sidelines of the central bank's board meeting in Kolkata.
"It is not going to happen immediately, it will happen in a staggered manner," he added.
The central bank deputy added it was not certain whether the Halkbank route to pay Iran had opened.
A senior official at Turkey's state-run Halkbank on Wednesday said it can only resume processing Indian oil payments to Iran once Western sanctions are officially lifted following an interim deal in Geneva last month.