In the latest Budget, Brown abolished Stamp Duty in a few deprived areas of the country, but the NAEA said this would only have a limited effect.
Hugh Dunsmore-Hardy, chief executive of the NAEA, said: "With house prices rising rapidly Stamp Duty is becoming an increasing burden for more and more homebuyers.
"The government’s latest changes give relief in only a few areas of the country. The reform we advocate would create a much fairer system and we will continue to press for substantial change in the next Budget.
"It will not create sufficient incentive for people or businesses to relocate to these areas and, meanwhile, the mass of the homebuying public will continue to be hit hard by this tax on moving."
The NAEA has proposed that the threshold at which Stamp Duty becomes applicable is raised from £60,000 to £100,000. It also wants a system of graduated charges so that properties that cost between £100,000 and £150,000 would pay 1.5 per cent on the value above the new exemption threshold, 2 per cent on £250-£500K, 2.5 per cent for those up to £750K, 3 per cent up to £1 million, 3.5 per cent up to £2 million and 4 per cent on those above £2 million.