The move would come into force from April 2015 when tax-raising powers would be given to the Scottish executive under the Scotland Act 2012.
The Stamp Duty proposals include changing the structure of the tax to a progressive system where the amount of tax paid is more closely related to the value of the property.
The government will launch two further consultations will be issued before the end of 2012.
Finance secretary John Swinney has also set up Revenue Scotland to collect certain taxes north of the border instead of HMRC.
Speaking at the Scottish parliament Swinney says the new property tax would focus more on the ability of the buyer to pay.
He says: “We have signalled our preference for a progressive system of taxation where the amount of tax paid is more closely related to the value of the property and therefore to the ability of the individual to pay.
“At the same time our consultation also indicates a willingness to adjust the threshold at which taxation is levied in order to support those at the lower end of the market.
The National Association of Estate Agents immediately welcomed the move to replace Stamp Duty
David Mackie, NAEA spokesperson for Scotland, is encouraged the Scottish government is looking at moving to a more progressive system.
He says: “We have long argued that the slab structure for Stamp Duty is unfair and creates huge distortions in the market, and we hope that the proposed ‘Land and Buildings Transaction Tax’ turns out to be a much fairer and more logical system.
“We applaud the Scottish Government for recognising the important role that housing provides in the wider economy and call on Westminster to follow suit.”