The new tax system is designed to be a "progressive" tax will have a progressive structure to bands and rates which is designed to remove the distortions in house prices associated with bunching of sales around the current thresholds SDLT.
The Land and Buildings Transaction Tax (LBTT) will ensure that while those buying a home under £180,000 will not pay any homeowner tax.
However, it is punitive for those purchasing property valued at more than £330,000 when the gap between SDLT costs and new LBTT starts to widen, Knight Frank forecasts show.
For example, a home worth £330,000 currently commands £9,900 under SDLT but £11,250 in LBTT.
There is a £7,000 difference at £450,000 and a 61pc hike in tax at £500,000.
The system is designed to stop a homeowner with a property worth £999,000 paying the same stamp duty as a property owner with a £500,001 house, but for the wealthier Scots this still means a considerable jump in their tax bill.
The Referendum had little impact in Edinburgh other than a slowing effect in the three weeks prior to the vote," said Edward Douglas-Home, Head of Knight Frank in Edinburgh.
"While we expect the market in Edinburgh to continue on its upward trajectory, this additional cost for buyers, particularly those buying north of £300,000, is likely to have an initial effect on the market, at least in the short term."
Ongoing negotiations between Holyrood and Westminster concerning further devolution and the upcoming May 2015 UK general election could create more uncertainty, he continued, especially when it comes to tax changes affecting high-value residential property.
Guidance on the new LBTT rates will be announced tomorrow (Thursday) moving away from the old British bandings which are as follows:
Below £125,000: 0pc
£125,001 - £250,000: 1pc
£250,001 - £500,000: 3pc
£500,001 - £1,000,000: 4pc
Andrew Peratt, head of Scotland and the North, for Savills, said: "There will be a purple patch for Scottish property in the short term, before the tax is switched in April 2015, but undoubtedly it will then take time for the market to adjust."
"More worrying is that it may be felt by vendors who may have to take the extra sum off the asking price. However there is still a compelling reason to buy in Scotland."
He added that this policy change was a "vote winner" as the majority of homes in Scotland are worth less than £180,000.