Does anyone know of a way to script secure file transfers that run automatically?

I support an output management system that can transfer print jobs to a system instead of a printer using FTP and a plain-text password file. Basically, when you send a print job to a queue that is an FTP destination, the output managment system kicks off a Perl script using the Net::FTP module to transfer the file, and it references the plain-text password file for the appropriate password for the destination system. The whole system right now makes me sick because of the plain-text passwords, and I'm trying to get around it by using scp instead. I'm having trouble getting around the password problem, though. It thought about including a line at the head of the Perl script to start an ssh-agent and run ssh-add to add an RSA or DSA authentication key created without a passphrase, but that would greatly compromise the account this is running under. Any other suggestions? This script has to be able to run automatically, without intervention.