It sounds like you are running under mod_perl. From the mod_perl manual:
Since the -T switch doesn't have an equivalent perl variable, mod_perl provides the PerlTaintCheck directive to turn on taint checks. In httpd.conf, enable this mode with:
Now any code compiled inside httpd will be taint checked.
If you use the -T switch, Perl will warn you that you should use the PerlTaintCheck configuration directive and will otherwise ignore it.
Now that means you have to have the authority to change your apache config files, and restart the server. I also imagine that all perl cgi programs that run under mod_perl then (check your scriptalias setting) will be taint checked - which may cause other programs to break.
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