From the libnet FAQ:
The FTP protocol does not have a command for changing the
permissions of a file on the remote server. But some ftp
servers may allow a chmod command to be issued via a SITE command, eg
$ftp->quot('site chmod 0777',$filename);
But this is not guaranteed to work.
Programmatically, I think you're going to hit a world of trouble trying to accomplish what you're trying to do... A hacky workaround would be to use Net::Telnet to go in after the files are at the remote site and issue the changes you desire... but that doesn't surmount the fact that most secure servers don't let users without superuser privledges chown files.
What is preventing you from logging into the remote host as the user you ultimatly want to own the files?