About to Close and I have a Size Problem

Not sure of your state laws or requirements (some states require a square footage disclosure at the time of the offer)  what I would do;  first I would ask you real estate agent for options....then you will have to decide if you want to call a real estate attorney.  Bets of Luck

Apparently there is no standard for how square footage is measured. This is why few agents actually list square footage on the mls in my area because of exactly what you are dealing with.

Some people measure to the outside wall, some count finished basement space (a no-no in NJ according to an appraiser who recently talked at an office meeting), some count foyer space-   there are many variables and it has never been standardized.

Only you can determine how important this issue is to you.  Seeking the adivce of an RE attorney may be a good idea but in the long run you have to decide whether or not walking away is something you are willing to do, if that becomes an option for you.

You need to consult a good RE attorney now before you close. 600 square feet is a big deal and can affect the marketability/value of the house down the line.

The appraisal may be right as far as value goes, but the appraiser's valuation may also be partially based on your willingness as the buyer to offer and pay that much to the seller. The appraisal cannot be relied upon and neither can your agent. Get legal advice now from someone who does not have an interest in this house closing. You might still have a reasonable deal, but you do need to explore your rights and come to terms with this one way or another before you close.

Don't get hung up on size - if the property appraised for more than you are paying for it, and the house size is less than you anticipated, do the math.   Have you paid too much, or did you get a deal in spite of the fact that the square footage differs?  Is the house as lovely as you thought it was before you knew that it didn't measure up?  If you used a Realtor for your purchase you probably have a contingency to get you out of  the deal - new disclosure, house does not measure up, 3 day right of recission.   You can try to re-negotiate (but you may loose the house), or you can just complete the transaction and feel good about it even though there is a difference between perception and reality. 

Sounds to me like you still don't really know exactly what you have.  Someone is wrong, but you don't really know who.  As a Realtor, we are supposed to have some idea of what a certain amount of square footage "feels like."  No way a competent agent is going to be off by almost 600 square feet.  In our MLS we are given an acceptable variance of 100 square feet, but in most cases, an agent should be able to get close.
 
This may be just me, but I see a red flag when the governing authority has exactly the same square footage as the agent.  This could mean the agent pulled the tax records and did not measure personally, which is NEVER a good idea unless dealing with multiple identical units--(like a large condo complex,) and even those can be off slightly.

Around here, the county government, when they measure for tax assessment, rounds to the nearest foot, so their measurements are almost always off.  Also, they report certain numbers as "heated square footage" that can be confused with total square footage that can contain the porches and decks and also rooms like sunrooms or below grade basements, or low ceilinged rooms that may not be heated or MAY not count for some other reason.  I have seen agents list space that is heated and cooled and finished that is located over a detached garage and they have counted it in the square footage, but according to MY MLS rules, if you can't enter the "bonus" space through heated and cooled space (a hallway of some kind) it cannot be counted.
Perhaps the discrepancy may be falling in the counting of rooms that do not qualify for "heated square footage" or perhaps one person who is measuring is counting something that the other person is not.  I would investigate if there
is basement area that was counted incorrectly or in our case at the beach, sometimes we don't count finished square footage downstairs if the home is located in the flood plain (our maps changed in 2006 so things were finished downstairs that were not in the flood plain then, but are now!) and may not be re-buildable or something like that.
I would start by asking my agent to measure the house, and ask for the listing agent's measuring diagram and also the appraiser's diagram and then compare them to figure out where and who is off!!  Most buyer's agents do not physically measure the house--at least in our market, because our MLS partners are the listing agents who are tasked with the responsibility of accurate measurement and then the appraiser is our "checks and balances" system.  Your MLS system should have a certain standard of measurements that it deems acceptable and they are not all the same in every MLS, so is it possible your appraiser has a different rule of measure from the MLS?  Many out of area appraisers are being used these days.  This is what I would be asking my agent if I were you, and consult your closing attorney for advice too. You need to be asking a lot of questions at this point.  Don't be afraid to ask your agent if there is someone else at their brokerage who would also be willing to measure the house.  On tough houses, my Broker in Charge is always willing to go and measure behind us to confirm the size.  I hope this helps.  Almost 600 sf is a really big deal!!!!  Good Luck!!!!!!

Holmes v. Summer: dilatory disclosures and the damage done
Read this article. Follow the link to the court case. You may have some recourse available. After reading that talking to the listing realtor and a lawyer may be a good idea.