NTFS

I’ve been asked by my supervisor to remove WinXP and install Win2000 on 6 pc’s. No problem right? Wrong, they want me to use FAT32, not NTFS. My teachings and limited experience teaches me that it can’t be done unless you use a 3rd party software. Am I wrong? If not, how do I go about this? Is it really worth doing? Don’t you loss disk integrity which can cause problems later?