"It is a settled law. The re-investigation or fresh investigation can be done only as per the directions of higher judiciary," the NIA said, adding that it had only conducted "further investigation" into the case.
The agency filed its reply after Dhan Singh, one of the accused arrested in the 2006 blasts case, had moved an application in the court last month saying that further investigation done by NIA is totally "illegal".
The accused had sought to know why and under whose directions the NIA had carried out an investigation, wherein they found the complicity of four accused, suspected to be members of a right wing extremist group.
"Whatever has been done by NIA, under the guise of further investigation is totally bad in law and hence the material collected by NIA has no legal sanctity," the application filed by him last month said.
"NIA is not a super agency which supersedes the earlier investigation (carried out by ATS and CBI) and all that is stated by NIA cannot be said to be above suspicion," it said.