Essentially, one my reference is unable for policy reasons is unable to give out his number (I don't know why, but this is answer I received). I know he has and will give me a good reference, but I am unsure how to point out the fact the potential employer will have to asked to be transferred to his current location which may depend on the time of day, that is he may be inside the facility or inside his office.
Edit: I should make a note that this reference must be included on the resume.
I have had this before, and you simply give them the public switchboard number. It's not uncommon at all to ring through on the public number and then ask for a specific person within the organisation.
In some ways that's a good thing, because it adds some level of credibility to the fact that your reference works at that organisation.
It sounds like you have a number to reach him at, it just isn't a direct number. It also sounds like you are not filling out a standardized form, but submitting a resume (and perhaps supporting information).
I'd recommend putting the contact information for your references on a separate page from the rest of your resume rather than trying to embed the information into the same structure as your resume. Simply give the name, title, and contact information that the person seeking the reference would use to initiate contact. Make a notation after the number stating that they are calling a reception desk or answering service (or whatever the number goes to) and will need to ask to be transferred.