The NCA said it was prompted by issues found with warrants in two cases that went before the courts, Operations Heterodon and Enderby.
Chris McKeogh, NCA deputy director, told the BBC the collapsed trials had been due to "incompetence".
It will review all warrants, production orders and account monitoring orders.
Authorisation for searches following arrest will also be looked at.
The issues came to light following an investigation by the news site Buzzfeed.
The NCA said it was "determined to ensure" the issues that affected these cases "are not repeated".
"It is a matter of record, and in those particular cases a harsh assessment but I think justified, to say that it was incompetence that sat within those two cases," Mr McKeogh told BBC Radio 4's Today programme.
The review is headed by a member of the NCA legal team, independent from the part of the NCA which obtained the warrant, and is assisted by the Crown Prosecution Service.
Mr McKeogh said by the time the review finishes, which is expected in January, they will have looked at "in excess of 2,000 different parts of documents that may be relevant to warrants and orders".
"The review started at the beginning of September and there has been nothing found to date that lets me, or indeed the senior panel that is doing this work with me - from the Crown Prosecution Service - to believe that we need to go back to settled cases," Mr McKeogh said.
"What we have got is, as we go through the various orders and documentation that we are finding, we are talking about small, technical, procedural flaws."
The NCA said it had issued updated guidance to officers and revised legal and awareness training for officers applying for warrants.
The National Crime Agency (NCA) has launched an internal inquiry into the way warrants are applied for following the collapse of major court trials.