Can I ask for a bit more detail about what you want to do? If you're actually trying to manipulate the time a cron job runs, then you could have the script bypass crontab and directly edit the crontab file. Of course you'd have to take extreme care not to bork the file otherwise cron won't understand it.
On the other hand, if you want to change what is being done, you're far better off setting up a shell script that the perl script edits and then having a crontab entry that runs that shell script at a given time. That way your perl script never has to worry about crontab.