In December, the average price paid for a home was £140,846, £6224 less than in the same month in 2011, a drop of 4.2%.
It is also the sixth consecutive monthly fall, with prices down more than £1000 from November.
Homes in Edinburgh experienced some of the sharpest declines as values fell by almost £17,000 annually.
However, the capital remains the most expensive area, with the average property costing £200,981.
East Renfrewshire is now the second most expensive place to buy, with an average price of £199,642.
Just nine of the country's 32 local authority areas recorded an increase, the latest LSL/Acad Scotland House Price Index shows.
Aberdeenshire, East Renfrewshire, Aberdeen, Argyll and Bute, Angus, Moray, Orkney, Dundee and Inverclyde all saw price rises from December 2011.
Richard Sexton, director of e.surv chartered surveyors, part of LSL, said: "Tough mortgage lending criteria and public-sector austerity hit the Scottish housing market hard last year.
"A lack of first-time buyer loans is the root cause of the Scottish market's ills.
"Mortgage lenders have married high deposit requirements with strict credit-scoring criteria, keeping would-be first-time buyers in rented accommodation.
"House prices in Scotland over the year have fallen by more than four times that of any region in England and Wales.
"Scotland's greater exposure to public-sector cuts is one reason. The other is the Bank of England's Funding for Lending scheme and its lack of impact north of the Border.
"The scheme has been far less effective in Scotland, making mortgages scarcer and more expensive."