The MHA had sought a report after Congress leader Digvijaya Singh asked Home Minister Sushil Kumar Shinde to clear the air on the issue.
The NIA has asked the Ministry of Home Affairs not to refer to Headley's statement in any other case, as it is part of the "sovereign assurance" given to the US, and it may affect the 26/11 probe.
"To the best of my knowledge, there is no mention of Ishrat in Headley's 117-page interrogation report submitted by NIA before me", said former home Secretary of India, G K Pillai.
The NIA is yet to trace the origin of the report which is being circulated as Headley's testimony in which he mentions Ishrat.
NIA informed the MHA that it had dismissed the report as "hearsay" and was yet to get any corroboration from the FBI.
(with agency inputs)