1. Fannie Mae is to pay transfer taxes
2. Fannie Mae is exempt from paying transfer taxes
3. Nowhere does it say you will be paying them
It seems that you would not be paying them. It's interesting, I am going over several HUD's for properties owned by Fannie Mae, several of them say "EXEMPT" on the transfer tax area, and some have the transfer taxes being paid by the buyer, and a few have them being paid by the seller. I also see that same:
"Seller to pay for Real Property Transfer Tax"
"Fannie Mae is a congressionally chartered corporation and is exempt from realty transfer taxes pursuant to 12 U.S.C. 1723a(c)(2)"
And on that same transaction Fannie Mae ended up paying the transfer taxes.
An interesting read on California Transfer Taxes, who is exempt, etc: http://www.hro.com/files/publications/Article-practice-guidev1.PDF "A PRACTICAL GUIDE TO TRANSFER TAXES IN CALIFORNIA"
I agree with Ron though, if your real estate agent doesn't know, your escrow company (or title, if you don't have a separate escrow company) can tell you specifically who will be paying them as they are the one who will be putting the fees on the closing statement at the end. If you are not at that point yet, and your real estate agent doesn't know, then I'd plan for the time being you are paying them until you get verification otherwise.