Yet smaller two-bedroom homes rose in value between January and February while high-end executive properties also increased.
But the NAEA said sellers across all ranges of property remained over-optimistic in their property asking prices.
NAEA chief executive Peter Bolton King said: "The NAEA’s property analysis reveals in depth what is happening in the housing market – and show how hard middle-class families in three-bedroom homes are being hit by the property slump.
"Smaller houses actually saw their value increase – this suggests that people who are buying are picking up smaller houses than they may have done previously, possibly because they can only get smaller mortgages. It may also reflect a trend of downsizing.
"The very top end of the market has also performed well, demonstrating not only that the very rich can still afford a high end property, but that with plummeting interest rates are now perhaps more tempted to put their money into bricks and mortar.
"Sellers are also consistently over-pricing their properties across the market, and inevitably having to accept a cut in price in order to achieve a sale."
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