Check in the PHP config file, you will find (or can add) this:
; This directive allows you to disable certain functions for security reasons.
; It receives a comma-delimited list of function names. This directive is
; NOT affected by whether Safe Mode is turned On or Off.
disable_functions =
NOTE: If you're trying to prevent users from running commands/external programs, you might look into disable additional functions such as [man]system[/man], [man]passthru[/man], and so on. Another alternative you can look into is safe_mode.