Process for Pharmacy Refills from Dr's. Office

I had an appointment with my family doc today for a minor health concern, and while I was there, asked about receiving the second Hepatitis A vaccine and getting a refill of my headache rx, which is a narcotic.

No problem accomplishing those items, but the process for refilling the prescription seemed strange to me.

Even though I was there and could have taken a written script to the pharmacy, I was asked to go to the drug store and have them fax the office to request the refill. When I stopped by the pharmacy, they said that was no problem, and took care of it right away. I was told to check back later this evening, and they expected to have my rx ready.

The reason given by the doctor's staff was simply to avoid confusion with paperwork. But that doesn't ring quite true to me. I realize that narcotic prescriptions must be handled with care, but I have a good rapport and long-standing relationship with the doc, and think she would talk to me if she suspected that I was overusing or abusing the rx.

Any insight as to why they handle refills this way?