The NTFS file system specification allows for complete data encryption, which gives users robust protection against unauthorized data access; only those who have a password can decrypt the data. On Windows platforms, FAT32 only supports rudimentary permission management on shared folders, while NTFS offers sophisticated permission management.
While individual files can be encrypted on any file system, NTFS supports system-wide encryption. This gives users a way to ensure that important documents are protected, so lapses in encryption protocol or vulnerabilities in encryption software cannot result in vulnerabilities.
Support for permission models with FAT32 varies based on the target operating system, but Windows operating systems generally allow only network-level permission management for shared folders. On multi-user systems, users looking to protect their information from other users have to encrypt their data.
In addition to providing better security against unauthorized access, NTFS also provides better file integrity security than FAT32. NTFS stores a log of data transactions; entries are stored before information is moved, erased or copied. Should the computer lose power during this transaction, the log can help restore lost information and complete the task. FAT32 partitions, on the other hand, are vulnerable to data corruption. This corruption is often fixable, but data can still be lost.