Disclosed herein are systems and methods for reducing a number of false positives in classification of files. In one aspect, an exemplary method comprises, analyzing a file to determine whether or not the file is to be recognized as being malicious, when the file is recognized as being malicious, analyzing the file to detect a false positive outcome, when the false positive outcome is detected, excluding the file from being scanned and calculating a flexible hash of the file, and storing the calculated flexible hash in a database of exceptions.