SNP faced renewed calls to revamp reform their controversial replacement for stamp duty
The Scottish Government has already confirmed a £793 million downgrade to estimates for the Land and Buildings Transaction Tax (LBTT).
But experts highlighted official figures suggesting receipts from the levy may fall even further in this and following financial years.
The warning came as Finance Secretary Derek Mackay's Budget for 2017/18 was signed-off by MSPs.
Mr Mackay struck a deal with the Greens to ensure his tax and spending plans passed their final parliamentary hurdle.
The government won the final vote by 68 to 57, with the Tories, Labour and Lib Dems voting against.
Mr Mackay has repeatedly rejected industry claims property sales have slumped since hitting buyers with a 10 per cent tax on homes worth more than £325,000.
In December it emerged that LBTT will bring £962million from standard residential sales.
This is £793million lower than its original forecast of £1.75billion.When commercial property income and the second homes tax are included, total revenue was forecast to be £2.2billion.
The SNP was well-warned about the unintended consequences its property tax changes would have
But an analysis of the latest Revenue Scotland figures show revenue dropped £16 million between December 2016 and January 2017 to £34.3 million.
The Scottish Property Federation (SPF) said it was now "very difficult" for the government to meet its LBTT forecast for 2016/17 and potentially in future years. The body also warned non-residential returns "are likely to be substantially less than they were in 2015/16".
Director David Melhuish said: “A weaker commercial property transaction market is the main driver behind these lower LBTT returns.
Finance Secretary Derek Mackay's Budget for 2017/18 has been signed-off by MSPs
"However, the failure to increase transactions and revenues at the higher value residential market is also weighing down on Scottish Government LBTT expectations."
House hunters pay LBTT on 2 per cent of the value of a home between £145,000 and £250,000, then 5 per cent from £250,000-£325,000, 10 per cent on £325,000-£750,000 and 12 per cent for all homes above £750,000.
Buyers of holiday homes, buy-to-let properties and any other second homes to pay an extra 3 per cent tax upfront – in addition to any other LBTT due.
The SPF wants the 5 per cent threshold lifted from £325,000 to £500,000 to boost sales of family homes.
Mr Mackay struck a deal with the Greens to ensure his tax and spending plans passed
Scottish Tory finance spokesman Murdo Fraser said: “The SNP was well-warned about the unintended consequences its property tax changes would have.
“And those cautions about the middle and upper ends of the market being jammed up are now coming to pass."
A Scottish Government spokesman said: "Our priority for LBTT remains helping first-time buyers enter the property market and assist people as they progress through the market.
"However, data shows that the market above £325,000 is not performing any differently relative to the market under £325,000.
"We continue to monitor all parts of the market closely and to engage with property sector stakeholders including the Scottish Property Federation."
Sturgeon's top moments Fri, December 9, 2016
Scotland's First Minister Nicola Sturgeon in pictures.
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Nicola Sturgeon visits Glaxo Smith Kline.
Meanwhile, Mr Mackay insisted his Budget will give Scots the "best deal" in the face of repeated accusations of damaging the economy.
Under the deal with the Greens he froze the the 40p rate of income at £43,000.
This will make around 360,000 higher rate taxpayers £400 a year worse off than people on similar salaries in other parts of the UK.
But he said the Budget will result in "£900 million of additional investment in our public services.