What is the best way to secure an intranet website developed using PHP
from outside attacks?
That's a stunningly thought-provoking question, and I'm surprised that you haven't received better answers.
Everything you would do for an external-facing application, and then some.
If I'm understanding you correctly, then you are asking a question which very few developers are asking themselves. Most companies have poor defence in depth, and once an attacker is in, he's in. Clearly you want to take it up a level.
So, what kind of attack are we thinking about?
If I'm the attacker and I'm attacking your intranet application, then I must have got access to your network somehow. This may not be as difficult as it sounds - I might try spearphishing (targetting email to individuals in your organisation, containing either malware attachements or links to sites which install malware) to get a trojan installed on an internal machine.
Once I've done this (and got control of an internal PC), I'll try all the same attacks I would try against any internet application.
However, that's not the end of the story. I've got more options: if I've got one of your user's PCs, then I might well be able to use a keylogger to gather usernames and passwords, as well as watching all your email for names and phone numbers.
Armed with these, I may be able to log into your application directly. I may even learn an admin username/password. Even if I don't, a list of names and phone numbers along with a feel for company lingo gives me a decent shot at socially engineering my way into wider access within your company.
The common answers to securing a web app: