As has already been pointed out, this isn't really a Perl specific question.

It could be that the direction was to use ftp to collect the script from the current machine and move to the new machine. The bad news is that ftp is hilariously insecure -- the username/password is sent in plaintext. Also, the ftp protocol is just used to transfer files (ftp stands File Transfer Protocol, in case you weren't aware); normally, there's no way for you to execute a script using ftp.

Once the script is moved to the new machine, you could set cron up to run the script at particular times, perhaps saving the result in a directory, possibly with a timestamp so that you could get datasets at difference times. Alternatively, cron could run on your local machine to run the script on the internal server.