small linux problem

my server was temporarily compromised and i guess whoever did it made it so that chmod or chown doesn't work. does anyone know how to fix this?

Your system is probably still compromised. Whoever broke into it most likely installed a number of back doors, root kits and the like. It would be hard to find all of those and since you don't seem to be a security expert, it will be pretty damn impossible for you.

Copy only files that are human readable off of the server, nuke it completely and set it up again. This time with security in mind from the start.