Figures from the tax office show the number of home sales tumbled over the year to September.
HMRC said there were 93,130 residential property transactions during the month, when adjusted for seasonal variations, down 11.3% from September 2016. The figure is provisional and may be revised.
"While the demand for homes continues to grow and interest rates are at a record low, the lack of properties available is reducing sales and driving up house prices," said Nick Davies, head of residential development at the estate agent Stirling Ackroyd.
Separate figures from HMRC show the amount of stamp duty collected in September on property purchases dropped 3.4% over the year to £927m ($1,130).
The housing market has been hit by affordability concerns for first-time buyers amid an ongoing shortage of homes, stamp duty hikes on buy-to-let investors and expensive houses, and uncertainty surrounding the vote for Brexit in the 23 June referendum.
But the Royal Institution of Chartered Surveyors (Rics) said the level of new buyer enquiries rose for the first time in seven months during September.
In its UK Residential Market Survey for the month, a net balance of 8% more respondents reported higher rather than lower demand, up from -5% in August and a substantial recovery from June's -34%.
"The market does now appear to be settling down following the significant headwinds encountered through the spring and summer," said Simon Rubinsohn, chief economist at Rics.
"Buyers do appear to be returning, albeit relatively slowly, but the big issue that continues to be highlighted by respondents is the lack of fresh stock on the market. Although this is not a new story, it is a significant one having ramifications for both prices and the level of turnover."