The last thing you want when buying a home is to pay too much. Yet that's exactly what many appraisers are now telling homebuyers they are doing -- often killing their prospects for mortgage loans in the process.

It's a slap in the face for buyers and sellers alike. Negotiating the right price for a home takes a huge amount of time and effort, as the parties go back and forth on various issues to come up with a price they can both agree on. After the buyer and the seller have successfully navigated the negotiation process, having a home appraiser put the brakes on a deal that both parties want runs counter to the whole free-market process.

Falling prices, tighter credit
Several factors are causing this tension between appraisers and homebuyers. The most important factor is where we are in the price cycle for real estate. Even though home prices are slipping in many areas of the country, sellers aren't giving up without a fight. Inventories of homes for sale are at historic highs, indicating that sellers have been content so far with longer waits to find buyers, rather than accepting fire-sale prices to sell their homes more quickly. While many of these sellers may eventually need to cut their listing prices to get their properties sold, some buyers are choosing not to wait for lower prices.

Meanwhile, although problems in the subprime mortgage market have remained contained thus far, even top lenders like JPMorgan Chase (NYSE:JPM) have started to tighten lending standards across the credit quality spectrum. Although there are many ways that lenders can tighten credit standards, demanding appraisals that reflect actual property values is the best way to make sure that even if borrowers default on their loans, the lender will recoup most or all of its money through foreclosure.

Appraisal: an inexact science
Unfortunately, the appraisal process itself is a tricky subject. Throughout the housing boom, some experts have accused disreputable real estate professionals of obtaining artificially high appraisals to obtain financing for high-price deals. Since many lenders and mortgage brokers immediately resold mortgage loans to other entities, including Freddie Mac (NYSE:FRE) and Fannie Mae (NYSE:FNM), they had every incentive to get deals done regardless of their economic viability. Now, some buyers are running into the opposite problem, as low-ball appraisals threaten their mortgage financing entirely.

Even though an appraisal has an exact dollar figure, the process is far from precise. The appraisal process lends itself to a combination of objective and subjective considerations. Although states require appraisers to obtain licenses and follow the established guidelines of national organizations like the American Society of Home Inspectors, most appraisals involve a subjective interpretation of what other properties are comparable to the home being appraised. By focusing on different factors, such as location, home size, and intangible characteristics such as views or desirable neighborhoods, appraisers can legitimately come to very different conclusions about the value of a given property.

What to do
If a low appraisal jeopardizes your real estate deal, don't panic. See if your lender will obtain a second appraisal. If not, then seek out another lender to see if you can find someone who's more willing to work with you. Of course, in some cases, your price will actually be higher than the home's fair market value. But you may still be able to go forward if you can make a larger down payment or get the seller to provide some financing to bridge the gap between what your lender's willing to loan you and what you're willing to pay.

For more information on finding and getting into the home of your dreams, be sure to look at our personal-finance service, Motley Fool Green Light. You can get free access to our Home Matters center, featuring articles on running the numbers on your mortgage, deciding on the right neighborhood for your family, and much more. You'll also find tips on buying, financing, and maintaining a home in the Fool's Home Center.

Fool contributor Dan Caplinger got a fair appraisal when he bought his house. He doesn't own shares of the companies mentioned in this article. JPMorgan Chase is a Motley Fool Income Investor pick. Fannie Mae is an Inside Value selection. The Fool's disclosure policy is like a roof over your head.