Hi,
makewhatis is part of the man package (man-1.5o1-7 on FC3 if I'm not mistaken), so if man works makewhatis must be (?) installed, typically here: /usr/sbin/makewhatis. It must be run as root, normal users will get a 'command not found' message.
If makewhatis is really missing or cannot be run as root try reinstalling the man package.
Hope this helps.
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