The Washington Post reported today that Fannie Mae will charge people more to get a home loan — even for those with perfect credit and can afford to put down a large down payment. The cost for a home loan may be even higher for those with less-than-perfect credit who do not have that much money upfront.

In a December 23, 2010 memo sent to lenders in its network, Fannie Mae announced that it has decided to impose a new schedule of higher add-on fees, similar to what Freddie Mac did just before Thanksgiving. The fee hikes are slated to go into effect this spring. Some potential buyers who have high credit scores and large down payments may be surprised to learn that they are also being targeted for higher “risk-based” fees, according to the Post article.

Let’s say someone wants to buy a house with a $300,000 first mortgage has a FICO score above 800 and just less than 25% cash for a down payment. In 2010, that person would not have to pay a loan fee because their down payment and credit score signified no risk of default. This year, Fannie Mae will tack on an extra quarter of a percentage point of the loan amount (in this case, $750).

If someone has a FICO score of 679 and can put down less than 20% for a down payment, that person would be assessed an add-on fee of 2.75%, or $8,250. Last year, that fee would have been $1,500 less.

In addition, Fannie and Freddie tack on what they call “adverse-market fees” of 0.75% of the loan, just for the privilege of sitting down with the lender. Using the $300,000 example, the cost would be $750. All the fees can be paid up front as part of the transaction costs or financed with a higher interest rate on the mortgage itself.

These fees are part of a multi-layered cumulative risk-based pricing system employed by Freddie and Fannie. Every perceived risk factor in a loan transaction receives its own separate add-on fee, and some fees are based on which type of real estate that is being financed. Condominiums are assessed higher fees than standalone houses (at 0.75% when the down payment is less than 25%). Rental investment properties, manufactured homes and loans with interest-only payment features all get separate fees, all of which mean significantly higher costs.

While Fannie Mae officials declined to comment on the reason for the fee hikes, Edward J. DeMarco, acting director of the agency overseeing Fannie and Freddie, said the add-ons were “necessary” to protect both lenders from “the costs and risks” inherent in the mortgages they buy or guarantee. The Post also reported that DeMarco said Fannie and Freddie “underpriced mortgage risks” during the housing market’s boom years.