are there advantages over doing it in php over perl?
Yes, it makes your boss happy. But that's not a question you should ask here. And you shouldn't ask it on a PHP forum either. Not that I don't think their answers would be biased - they aren't useful for you. You don't want to do it in PHP - your boss does. So, ask you boss what the advantages are. It doesn't matter whether what he thinks are advantages are really advantages, but as long as he thinks they are, those are the arguments you have to deal with.
Which is more secure?
Neither. It's an irrelevant question. Programs are secure or not. You can write secure programs in any language (and it's difficult in all of them), and you can write insecure programs in any language (and that's surprisingly easy).
Will I have a difficult time since I've done almost no php?
How can we know? Some people pick up new languages in a matter of hours. Others are stuck in the first language they've learned, and will never become good in any other.
You're not asking the right question - and you're not asking them to the right people either.