If you encrypted the password, you'd presumably then have to have a password to decrypt it and you're right back where you started from. Start by making the source only readable by the narrowest possible amount of people (possibly by making it setuid, but make sure you've read perldoc perlsec and trim the privileged code down to the bare minimum to get the job done). You could also use a source filter, but that also has limitations (see perldoc -q "hide the source").
Depending on the application you might be able to use some other means of getting the password to your application (for instance running it under ssh-agent) or running as a different user (sudo or the like). More details about what you need the password for might help people steer you towards a more applicable solution.
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